Publications
Selected publications
- Applications of contact predictions to structural biology (Journal article - 2017)
- The 2022 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection (Journal article - 2022)
- Assessing the utility of CASP14 models for molecular replacement (Journal article - 2021)
- Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications (Journal article - 2021)
- High-accuracy protein structure prediction in CASP14 (Journal article - 2021)
- Prophages encode phage-defense systems with cognate self-immunity (Journal article - 2021)
- In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. (Journal article - 2021)
- Using Phaser and ensembles to improve the performance of SIMBAD (Journal article - 2020)
- findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM (Journal article - 2022)
- Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM (Journal article - 2021)
2024
Interpretable deep cross networks unveiled common signatures of dysregulated epitranscriptomes across 12 cancer types.
Xia, R., Yin, X., Huang, J., Chen, K., Ma, J., Wei, Z., . . . Song, B. (2024). Interpretable deep cross networks unveiled common signatures of dysregulated epitranscriptomes across 12 cancer types.. Molecular therapy. Nucleic acids, 35(4), 102376. doi:10.1016/j.omtn.2024.102376
Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation.
Wang, H., Wang, Y., Zhou, J., Song, B., Tu, G., Nguyen, A., . . . Meng, J. (2024). Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation.. Cell genomics, 100702. doi:10.1016/j.xgen.2024.100702
The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era.
Keegan, R. M., Simpkin, A. J., & Rigden, D. J. (2024). The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era.. Acta crystallographica. Section D, Structural biology, 80(Pt 11), 766-779. doi:10.1107/s2059798324009380
Using deep-learning predictions reveals a large number of register errors in PDB depositions.
Sánchez Rodríguez, F., Simpkin, A. J., Chojnowski, G., Keegan, R. M., & Rigden, D. J. (2024). Using deep-learning predictions reveals a large number of register errors in PDB depositions.. IUCrJ. doi:10.1107/s2052252524009114
AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins
m6AConquer: a Data Resource for Unified Quantification and Integration of m6A Detection Techniques
Functional Characterization of Splice Variants in the Diagnosis of Albinism.
Diallo, M., Courdier, C., Mercier, E., Sequeira, A., Defay-Stinat, A., Plaisant, C., . . . Arveiler, B. (2024). Functional Characterization of Splice Variants in the Diagnosis of Albinism.. International journal of molecular sciences, 25(16), 8657. doi:10.3390/ijms25168657
Investigating Medin Cleavage Accessibility in MfgE8: Conformational Insights Derived from Molecular Dynamics Simulations and AlphaFold2 Models
m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq.
Ye, H., Li, T., Rigden, D. J., & Wei, Z. (2024). m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq.. Nucleic acids research, gkae280. doi:10.1093/nar/gkae280
Deep-learning protein structure predictions suggest likely molecular functions for three uncharacterised polytopic membrane proteins from the<i>P. falciparum</i>apicoplast
The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.
Rigden, D. J., & Fernández, X. M. (2024). The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.. Nucleic acids research, 52(D1), D1-D9. doi:10.1093/nar/gkad1173
KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival.
Saleh, H., Liloglou, T., Rigden, D. J., Parsons, J. L., & Grundy, G. J. (2024). KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival.. Journal of molecular biology, 436(4), 168434. doi:10.1016/j.jmb.2023.168434
2023
Microtubule association of TRIM3 revealed by differential extraction proteomics.
Glover, H. L., Mendes, M., Gomes-Neto, J., Rusilowicz-Jones, E. V., Rigden, D. J., Dittmar, G., . . . Clague, M. J. (2023). Microtubule association of TRIM3 revealed by differential extraction proteomics.. Journal of cell science, jcs.261522. doi:10.1242/jcs.261522
Assessment of three-dimensional RNA structure prediction in CASP15.
Das, R., Kretsch, R. C., Simpkin, A. J., Mulvaney, T., Pham, P., Rangan, R., . . . Westhof, E. (2023). Assessment of three-dimensional RNA structure prediction in CASP15.. Proteins, 91(12), 1747-1770. doi:10.1002/prot.26602
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15.
Kryshtafovych, A., Montelione, G. T., Rigden, D. J., Mesdaghi, S., Karaca, E., & Moult, J. (2023). Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15.. Proteins, 91(12), 1903-1911. doi:10.1002/prot.26584
CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.
Mulvaney, T., Kretsch, R. C., Elliott, L., Beton, J. G., Kryshtafovych, A., Rigden, D. J., . . . Topf, M. (2023). CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.. Proteins, 91(12), 1935-1951. doi:10.1002/prot.26644
Tertiary structure assessment at CASP15
Simpkin, A. J., Mesdaghi, S., Rodriguez, F. S., Elliott, L., Murphy, D. L., Kryshtafovych, A., . . . Rigden, D. J. (2023). Tertiary structure assessment at CASP15. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. doi:10.1002/prot.26593
m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m<SUP>7</SUP>G) epitranscriptome
Wang, X., Zhang, Y., Chen, K., Liang, Z., Ma, J., Xia, R., . . . Song, B. (2023). m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m<SUP>7</SUP>G) epitranscriptome. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkad789
Predicted models and <i>CCP</i>4
Simpkin, A. J., Caballero, I., McNicholas, S., Stevenson, K., Jimenez, E., Rodriguez, F. S., . . . Keegan, R. M. (2023). Predicted models and <i>CCP</i>4. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 79, 806-819. doi:10.1107/S2059798323006289
Engineering a Carboxyl Methyltransferase for the Formation of a Furan-Based Bioplastic Precursor
Ward, L. C., Goulding, E., Rigden, D. J., Allan, F. E., Pellis, A., Hatton, H., . . . Carnell, A. J. (2023). Engineering a Carboxyl Methyltransferase for the Formation of a Furan-Based Bioplastic Precursor. CHEMSUSCHEM. doi:10.1002/cssc.202300516
m(6) A-Atlas v2.0: updated resources for unraveling the N 6-methyladenosine (m(6)A) epitranscriptome among multiple species
Liang, Z., Ye, H., Ma, J., Wei, Z., Wang, Y., Zhang, Y., . . . Chen, K. (2023). m(6) A-Atlas v2.0: updated resources for unraveling the N 6-methyladenosine (m(6)A) epitranscriptome among multiple species. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkad691
CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps.
Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space
Mesdaghi, S., Price, R. M., Madine, J., & Rigden, D. J. (2023). Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space. Journal of Structural Biology, 108010. doi:10.1016/j.jsb.2023.108010
m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues.
Song, B., Huang, D., Zhang, Y., Wei, Z., Su, J., Pedro de Magalhães, J., . . . Chen, K. (2023). m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues.. Genomics, proteomics & bioinformatics, 21(4), 678-694. doi:10.1016/j.gpb.2022.09.001
Structural Insights into Pink-eyed Dilution Protein (Oca2).
Mesdaghi, S., Murphy, D. L., Simpkin, A. J., & Rigden, D. J. (2023). Structural Insights into Pink-eyed Dilution Protein (Oca2).. Bioscience reports, BSR20230060. doi:10.1042/bsr20230060
CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps
The <i>CCP4</i> suite: integrative software for macromolecular crystallography
Agirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Basle, A., Beilsten-Edmands, J., . . . Yamashita, K. (2023). The <i>CCP4</i> suite: integrative software for macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 79, 449-461. doi:10.1107/S2059798323003595
To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units
Kryshtafovych, A., & Rigden, D. J. (2023). To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. doi:10.1002/prot.26533
Tertiary structure assessment at CASP15
An exonuclease V homologue is expressed predominantly during early megasporogenesis in apomictic Brachiaria brizantha.
Dusi, D. M. A., Alves, E. R., Cabral, G. B., Mello, L. V., Rigden, D. J., Silveira, É. D., . . . Carneiro, V. T. C. (2023). An exonuclease V homologue is expressed predominantly during early megasporogenesis in apomictic Brachiaria brizantha.. Planta, 258(1), 5. doi:10.1007/s00425-023-04162-8
To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units
RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication
Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., . . . Wei, Z. (2023). RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. NUCLEIC ACIDS RESEARCH, 51(D1), D1388-D1396. doi:10.1093/nar/gkac750
The 2023 <i>Nucleic Acids</i> <i>Research</i> Database Issue and the online molecular biology database collection
Rigden, D. J., & Fernandez, X. M. (2023). The 2023 <i>Nucleic Acids</i> <i>Research</i> Database Issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 51(D1), D1-D8. doi:10.1093/nar/gkac1186
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Zhang, Y., Jiang, J., Ma, J., Wei, Z., Wang, Y., Song, B., . . . Chen, K. (2023). DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.. Nucleic Acids Res., 51, 106-116.
2022
Structural Insights into Pink-eyed Dilution Protein (Oca2)
Using deep-learning predictions of inter-residue distances for model validation
Rodriguez, F. S., Chojnowski, G., Keegan, R. M., & Rigden, D. J. (2022). Using deep-learning predictions of inter-residue distances for model validation. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78, 1412-1427. doi:10.1107/S2059798322010415
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Zhang, Y., Jiang, J., Ma, J., Wei, Z., Wang, Y., Song, B., . . . Chen, K. (2022). DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.. Nucleic acids research, gkac1061. doi:10.1093/nar/gkac1061
Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation
Huang, D., Chen, K., Song, B., Wei, Z., Su, J., Coenen, F., . . . Meng, J. (2022). Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation. NUCLEIC ACIDS RESEARCH, 50(18), 10290-10310. doi:10.1093/nar/gkac830
<i>CCP</i>4 Cloud for structure determination and project management in macromolecular crystallograpny
Krissinel, E., Lebedev, A. A., Uski, V., Ballard, C. B., Keegan, R. M., Kovalevskiy, O., . . . Brown, D. G. (2022). <i>CCP</i>4 Cloud for structure determination and project management in macromolecular crystallograpny. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78, 1079-1089. doi:10.1107/S2059798322007987
Using deep learning predictions of inter-residue distances for model validation
<i>Slice'N'Dice</i>: maximising predicted models for structural biologists
Simpkin, A. J., Elliot, L. G., Rigden, D. J., & Keegan, R. M. (2022). <i>Slice'N'Dice</i>: maximising predicted models for structural biologists. Acta Crystallographica Section A Foundations and Advances, 78(a2), e24. doi:10.1107/s2053273322096474
Evolutionary covariance to assess the biological relevance of putative homo-oligomeric interfaces
Burgos-Marmol, J. J., Keegan, R. M., Krissinel, E., & Rigden, D. J. (2022). Evolutionary covariance to assess the biological relevance of putative homo-oligomeric interfaces. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 78 (pp. E434). Retrieved from https://www.webofscience.com/
PDB-wide model validation using deep learning based predictions of distances and contacts
Sanchez Rodriguez, F., Chojnowski, G., Keegan, R., & Rigden, D. (2022). PDB-wide model validation using deep learning based predictions of distances and contacts. Acta Crystallographica Section A Foundations and Advances, 78(a2), e79. doi:10.1107/s2053273322095997
Slice'N'Dice: maximising predicted models for structural biologists
Simpkin, A. J., Elliot, L. G., Rigden, D. J., & Keegan, R. M. (2022). Slice'N'Dice: maximising predicted models for structural biologists. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 78 (pp. E24). doi:10.1107/S2053273322096462
Slice’N’Dice: Maximising the value of predicted models for structural biologists
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction
Liu, L., Song, B., Chen, K., Zhang, Y., de Magalhaes, J. P., Rigden, D. J., . . . Wei, Z. (2022). WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction. METHODS, 203, 378-382. doi:10.1016/j.ymeth.2021.07.003
<i>MrParse:</i> finding homologues in the PDB and the EBI AlphaFold database tor molecular replacement and more
Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2022). <i>MrParse:</i> finding homologues in the PDB and the EBI AlphaFold database tor molecular replacement and more. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78, 553-559. doi:10.1107/S2059798322003576
Carboxyl Methyltransferase Catalysed Formation of Mono- and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis
Ward, L. C., McCue, H. V., Rigden, D. J., Kershaw, N. M., Ashbrook, C., Hatton, H., . . . Carnell, A. J. (2022). Carboxyl Methyltransferase Catalysed Formation of Mono- and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 61(14). doi:10.1002/anie.202117324
Carboxyl Methyltransferase Catalysed Formation of Mono‐ and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis
Ward, L. C., McCue, H. V., Rigden, D. J., Kershaw, N. M., Ashbrook, C., Hatton, H., . . . Carnell, A. J. (2022). Carboxyl Methyltransferase Catalysed Formation of Mono‐ and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis. Angewandte Chemie, 134(14). doi:10.1002/ange.202117324
Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs
Bengtsson, R. J., Simpkin, A. J., Pulford, C. V., Low, R., Rasko, D. A., Rigden, D. J., . . . Baker, K. S. (2022). Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. NATURE MICROBIOLOGY. doi:10.1038/s41564-021-01054-z
m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues
The 2022 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection
Rigden, D. J., & Fernandez, X. M. (2022). The 2022 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 50(D1), D1-D10. doi:10.1093/nar/gkab1195
m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.
Ma, J., Song, B., Wei, Z., Huang, D., Zhang, Y., Su, J., . . . Chen, K. (2022). m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.. Nucleic acids research, 50(D1), D196-D203. doi:10.1093/nar/gkab1075
Epitranscriptome data integration and functional prediction using complex networks and machine learning approaches
Tang, Y. (2022). Epitranscriptome data integration and functional prediction using complex networks and machine learning approaches.
findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM
Chojnowski, G., Simpkin, A. J., Leonardo, D. A., Seifert-Davila, W., Vivas-Ruiz, D. E., Keegan, R. M., & Rigden, D. J. (2022). findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCrJ, 9(1), 86-97. doi:10.1107/s2052252521011088
2021
Assessing the utility of CASP14 models for molecular replacement
Millan, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., . . . Read, R. J. (2021). Assessing the utility of CASP14 models for molecular replacement. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89(12), 1752-1769. doi:10.1002/prot.26214
Evaluation of model refinement in CASP14
Simpkin, A. J., Sanchez Rodriguez, F., Mesdaghi, S., Kryshtafovych, A., & Rigden, D. J. (2021). Evaluation of model refinement in CASP14. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89(12), 1852-1869. doi:10.1002/prot.26185
High-accuracy protein structure prediction in CASP14
Pereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M., & Lupas, A. N. (2021). High-accuracy protein structure prediction in CASP14. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89(12), 1687-1699. doi:10.1002/prot.26171
Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions
Moroz, O. V., Blagova, E., Lebedev, A. A., Rodriguez, F. S., Rigden, D. J., Tams, J. W., . . . Wilson, K. S. (2021). Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 77, 1564-1578. doi:10.1107/S2059798321010949
The X-ray structure of juvenile hormone diol kinase from the silkworm <i>Bombyx mori</i>
Guo, J., Keegan, R. M., Rigden, D. J., Erskine, P. T., Wood, S. P., Li, S., & Cooper, J. B. (2021). The X-ray structure of juvenile hormone diol kinase from the silkworm <i>Bombyx mori</i>. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 77, 465-472. doi:10.1107/S2053230X21012012
Prophages encode phage-defense systems with cognate self-immunity
Owen, S. V., Wenner, N., Dulberger, C. L., Rodwell, E. V., Bowers-Barnard, A., Quinones-Olvera, N., . . . Hinton, J. C. D. (2021). Prophages encode phage-defense systems with cognate self-immunity. CELL HOST & MICROBE, 29(11), 1620-+. doi:10.1016/j.chom.2021.09.002
ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome
Song, B., Chen, K., Tang, Y., Wei, Z., Su, J., de Magalhaes, J. P., . . . Meng, J. (2021). ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. BRIEFINGS IN BIOINFORMATICS, 22(6). doi:10.1093/bib/bbab088
Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM
Simpkin, A. J., Winn, M. D., Rigden, D. J., & Keegan, R. M. (2021). Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 77, 1378-1385. doi:10.1107/S2059798321009165
MrParse: Finding homologues in the PDB and the EBI AlphaFold database for Molecular Replacement and more
Applications of residue contact predictions in structural biology
Rodriguez, F. S., Keegan, R. M., Vollmar, M., Evans, G., & Rigden, D. J. (2021). Applications of residue contact predictions in structural biology. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 77 (pp. C48). Retrieved from https://www.webofscience.com/
Exploiting new generation ab initio and homology models from databases for MR
Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2021). Exploiting new generation ab initio and homology models from databases for MR. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 77 (pp. C688). Retrieved from https://www.webofscience.com/
PISACov: Expanding jsPISA with evolutionary covariance data to better determine protein quaternary state from a crystal structure
Burgos-Marmol, J. J., Keegan, R. M., Krissinel, E., & Rigden, D. J. (2021). PISACov: Expanding jsPISA with evolutionary covariance data to better determine protein quaternary state from a crystal structure. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 77 (pp. C693). Retrieved from https://www.webofscience.com/
Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications
Song, Z., Huang, D., Song, B., Chen, K., Song, Y., Liu, G., . . . Meng, J. (2021). Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-24313-3
Assessing the utility of CASP14 models for molecular replacement
Assessing the utility of CASP14 models for molecular replacement
Informing shigellosis prevention and control through pathogen genomics
<i>Bodo saltans</i> (Kinetoplastida) is dependent on a novel <i>Paracaedibacter</i>-like endosymbiont that possesses multiple putative toxin-antitoxin systems
Midha, S., Rigden, D. J., Siozios, S., Hurst, G. D. D., & Jackson, A. P. (2021). <i>Bodo saltans</i> (Kinetoplastida) is dependent on a novel <i>Paracaedibacter</i>-like endosymbiont that possesses multiple putative toxin-antitoxin systems. ISME JOURNAL, 15(6), 1680-1694. doi:10.1038/s41396-020-00879-6
Bisphenol A Inhibits the Transporter Function of the Blood-Brain Barrier by Directly Interacting with the ABC Transporter Breast Cancer Resistance Protein (BCRP)
Engdahl, E., van Schijndel, M. D. M., Voulgaris, D., Di Criscio, M., Ramsbottom, K. A., Rigden, D. J., . . . Ruegg, J. (2021). Bisphenol A Inhibits the Transporter Function of the Blood-Brain Barrier by Directly Interacting with the ABC Transporter Breast Cancer Resistance Protein (BCRP). INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 22(11). doi:10.3390/ijms22115534
Evaluation of model refinement in CASP14
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer
Edogbanya, J., Tejada-Martinez, D., Jones, N. J., Jaiswal, A., Bell, S., Cordeiro, R., . . . de Magalhaes, J. P. (2021). Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. CELLULAR AND MOLECULAR LIFE SCIENCES, 78(9), 4365-4376. doi:10.1007/s00018-021-03789-8
Identification of unknown proteins in X-ray crystallography and cryo-EM
ConPlot: web-based application for the visualization of protein contact maps integrated with other data
Rodriguez, F. S., Mesdaghi, S., Simpkin, A. J., Burgos-Marmol, J. J., Murphy, D. L., Uski, V., . . . Rigden, D. J. (2021). ConPlot: web-based application for the visualization of protein contact maps integrated with other data. BIOINFORMATICS, 37(17), 2763-2765. doi:10.1093/bioinformatics/btab049
RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis
Chen, K., Song, B., Tang, Y., Wei, Z., Xu, Q., Su, J., . . . Meng, J. (2021). RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. NUCLEIC ACIDS RESEARCH, 49(D1), D1396-D1404. doi:10.1093/nar/gkaa790
The 2021 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection
Rigden, D. J., & Fernandez, X. M. (2021). The 2021 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 49(D1), D1-D9. doi:10.1093/nar/gkaa1216
m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome
Tang, Y., Chen, K., Song, B., Ma, J., Wu, X., Xu, Q., . . . Meng, J. (2021). m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome. NUCLEIC ACIDS RESEARCH, 49(D1), D134-D143. doi:10.1093/nar/gkaa692
ConPlot: web-based application for the visualization of protein contact maps integrated with other data.
Rodríguez, F. S., Mesdaghi, S., Simpkin, A. J., Burgos-Mármol, J. J., Murphy, D. L., Uski, V., . . . Rigden, D. J. (2021). ConPlot: web-based application for the visualization of protein contact maps integrated with other data.. Bioinform., 37, 2763-2765.
In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b.
Mesdaghi, S., Murphy, D. L., Sánchez Rodríguez, F., Burgos-Mármol, J. J., & Rigden, D. J. (2020). In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b.. F1000Research, 9, 1395. doi:10.12688/f1000research.27676.2
2020
Helical ensembles outperform ideal helices in molecular replacement
Sanchez Rodriguez, F., Simpkin, A. J., Davies, O. R., Keegan, R. M., & Rigden, D. J. (2020). Helical ensembles outperform ideal helices in molecular replacement. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 76, 962-970. doi:10.1107/S205979832001133X
Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Φ24<sub>B</sub>
Franke, B., Veses-Garcia, M., Diederichs, K., Allison, H., Rigden, D. J., & Mayans, O. (2020). Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Φ24<sub>B</sub>. JOURNAL OF STRUCTURAL BIOLOGY, 212(1). doi:10.1016/j.jsb.2020.107596
The<i>Paracaedibacter</i>-like endosymbiont of<i>Bodo saltans</i>(Kinetoplastida) uses multiple putative toxin-antitoxin systems to maintain its host association
Maturation of the functional mouse CRES amyloid from globular form
Hewetson, A., Khan, N. H., Dominguez, M. J., Do, H. Q., Kusko, R. E., Borcik, C. G., . . . Cornwall, G. A. (2020). Maturation of the functional mouse CRES amyloid from globular form. Proceedings of the National Academy of Sciences of the United States of America, 117(28), 16363-16372. doi:10.1073/pnas.2006887117
Prophage-encoded phage defense proteins with cognate self-immunity
Owen, S., Wenner, N., Dulberger, C., Rodwell, E., Bowers-Barnard, A., Quinones-Olvera, N., . . . Hinton, J. (2020). Prophage-encoded phage defense proteins with cognate self-immunity. doi:10.1101/2020.07.13.199331
In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b
Helical ensembles out-perform ideal helices in Molecular Replacement
Rodríguez, F. S., Simpkin, A., Davies, O., Keegan, R., & Rigden, D. (2020). Helical ensembles out-perform ideal helices in Molecular Replacement. doi:10.1101/2020.06.16.154690
m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human
Song, B., Tang, Y., Chen, K., Wei, Z., Rong, R., Lu, Z., . . . Meng, J. (2020). m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Bioinformatics, 36(11), 3528-3536. doi:10.1093/bioinformatics/btaa178
The importance of chain context in assessing small nucleotide variants in titin: in silico case study of the I10 - I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580.
Rigden, D., Fleming, J., & Mayans, O. (2020). The importance of chain context in assessing small nucleotide variants in titin: in silico case study of the I10 - I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580.. Journal of Biomolecular Structure and Dynamics.
Extending the scope of coiled-coil crystal structure solution by <i>AMPLE</i> through improved <i>ab initio</i> modelling
Thomas, J. M. H., Keegan, R. M., Rigden, D. J., & Davies, O. R. (2020). Extending the scope of coiled-coil crystal structure solution by <i>AMPLE</i> through improved <i>ab initio</i> modelling. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 76, 272-284. doi:10.1107/S2059798320000443
Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles
Ramsbottom, K. A., Carr, D. F., Rigden, D. J., & Jones, A. R. (2020). Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles. PLOS ONE, 15(2). doi:10.1371/journal.pone.0220754
The 27th annual Nucleic Acids Research database issue and molecular biology database collection
Rigden, D. J., & Fernandez, X. M. (2020). The 27th annual Nucleic Acids Research database issue and molecular biology database collection. NUCLEIC ACIDS RESEARCH, 48(D1), D1-D8. doi:10.1093/nar/gkz1161
Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics
Liu, L., Song, B., Ma, J., Song, Y., Zhang, S. -Y., Tang, Y., . . . Meng, J. (2020). Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18, 1587-1604. doi:10.1016/j.csbj.2020.06.010
Exploring unconventional approaches to Molecular Replacement in X-ray crystallography with SIMBAD
Simpkin, A. (2020). Exploring unconventional approaches to Molecular Replacement in X-ray crystallography with SIMBAD.
Informatics investigations into HLA-mediated adverse drug reactions
Ramsbottom, K. (2020). Informatics investigations into HLA-mediated adverse drug reactions.
Protein Phosphohistidine Phosphatases of the HP Superfamily
Rigden, D. J. (2020). Protein Phosphohistidine Phosphatases of the HP Superfamily. In HISTIDINE PHOSPHORYLATION (Vol. 2077, pp. 93-107). doi:10.1007/978-1-4939-9884-5_7
Using Phaser and ensembles to improve the performance of SIMBAD
Simpkin, A., Simkovic, F., Thomas, J., Savko, M., Lebedev, A., Uski, V., . . . Keegan, R. (n.d.). Using Phaser and ensembles to improve the performance of SIMBAD. Acta Crystallographica Section D: Biological Crystallography.
2019
Molecular replacement using structure predictions from databases
Simpkin, A. J., Thomas, J. M. H., Simkovic, F., Keegan, R. M., & Rigden, D. J. (2019). Molecular replacement using structure predictions from databases. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 75, 1051-1062. doi:10.1107/S2059798319013962
MOLECULAR REPLACEMENT MODEL PREPARATION AND ITS AUTOMATION IN MORDA AND MRBUMP
Lebedev, A., Vagin, A., McNicholas, S., Thomas, J., Uski, V., Rigden, D., & Keegan, R. (2019). MOLECULAR REPLACEMENT MODEL PREPARATION AND ITS AUTOMATION IN MORDA AND MRBUMP. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 75 (pp. E158). doi:10.1107/S2053273319093987
MOLECULAR REPLACEMENT USING STRUCTURE PREDICTIONS FROM NEW GENERATION DATABASES
Rigden, D., Simpkin, A., Thomas, J., Simkovic, F., & Keegan, R. (2019). MOLECULAR REPLACEMENT USING STRUCTURE PREDICTIONS FROM NEW GENERATION DATABASES. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 75 (pp. E183). doi:10.1107/S2053273319093732
NEW COVARIANCE-BASED METHODS FOR UNCONVENTIONAL MR OF TRANSMEMBRANE PROTEINS
Rodriguez, S. F., Rigden, D., Keegan, R., Evans, G., & Vollmar, M. (2019). NEW COVARIANCE-BASED METHODS FOR UNCONVENTIONAL MR OF TRANSMEMBRANE PROTEINS. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 75 (pp. E191). doi:10.1107/S2053273319093653
SIMBAD: STRUCTURE BASED SEARCH MODEL IDENTIFICATION FOR MOLECULAR REPLACEMENT USING THE PDB DATABASE
Simpkin, A., Simkovic, F., Thomas, J., Savko, M., Lebedev, A., Uski, V., . . . Keegan, R. (2019). SIMBAD: STRUCTURE BASED SEARCH MODEL IDENTIFICATION FOR MOLECULAR REPLACEMENT USING THE PDB DATABASE. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 75 (pp. E177). doi:10.1107/S2053273319093793
Informatics investigations into anti-thyroid drug induced agranulocytosis associated with multiple HLA-B alleles
The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis
Nunes, Q. M., Su, D., Brownridge, P. J., Simpson, D. M., Sun, C., Li, Y., . . . Fernig, D. G. (2019). The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis. PLOS ONE, 14(6). doi:10.1371/journal.pone.0217633
WHISTLE: a high-accuracy map of the human N<SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome predicted using a machine learning approach
Chen, K., Wei, Z., Zhang, Q., Wu, X., Rong, R., Lu, Z., . . . Meng, J. (2019). WHISTLE: a high-accuracy map of the human N<SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome predicted using a machine learning approach. NUCLEIC ACIDS RESEARCH, 47(7). doi:10.1093/nar/gkz074
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection
Rigden, D. J., & Fernandez, X. M. (2019). The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. NUCLEIC ACIDS RESEARCH, 47(D1), D1-D7. doi:10.1093/nar/gky1267
2018
Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions
Ramsbottom, K. A., Carr, D. F., Jones, A. R., & Rigden, D. J. (2018). Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with adverse drug reactions. MOLECULAR IMMUNOLOGY, 101, 488-499. doi:10.1016/j.molimm.2018.08.003
Ensembling for molecular replacement: making the most of your distant homologues
Keegan, R., Rigden, D., McNicholas, S., Krissinel, E., Thomas, J., Simpkin, A., . . . Wilson, K. (2018). Ensembling for molecular replacement: making the most of your distant homologues. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 74 (pp. E175). doi:10.1107/S2053273318092586
Exploiting residue-residue contact information beyond structure predictions in Molecular Replacement
Simkovic, F., de Oliveira, S., Deane, C., & Rigden, D. J. (2018). Exploiting residue-residue contact information beyond structure predictions in Molecular Replacement. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 74 (pp. E46). doi:10.1107/S2053273318094500
Exploiting residue–residue contact information beyond structure predictions in molecular replacement
Simkovic, F., de Oliveira, S., Deane, C., & Rigden, D. J. (2018). Exploiting residue–residue contact information beyond structure predictions in molecular replacement. Acta Crystallographica Section A Foundations and Advances, 74(a2), e46. doi:10.1107/s2053273318094512
Identification of contaminants with SIMBAD: A Sequence-independent molecular replacement pipeline
Simpkin, A., Simkovic, F., Thomas, J., Savko, M., Ballard, C., Wojdyr, M., . . . Keegan, R. (2018). Identification of contaminants with SIMBAD: A Sequence-independent molecular replacement pipeline. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 74 (pp. E172). doi:10.1107/S2053273318092641
SIMBAD: A Sequence-independent molecular-replacement pipeline
Simpkin, A., Simkovic, F., Thomas, J., Savko, M., Lebedev, A., Uski, V., . . . Keegan, R. (2018). SIMBAD: A Sequence-independent molecular-replacement pipeline. Acta Crystallographica Section D: Structural Biology, 74(7), 595-605. doi:10.1107/S2059798318005752
Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds
Kozic, M., Fox, S. J., Thomas, J. M., Verma, C. S., & Rigden, D. J. (2018). Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 86(5), 548-565. doi:10.1002/prot.25473
Critical assessment of approaches for molecular docking to elucidate associations of HLA alleles with Adverse Drug Reactions
Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance
Isaacs, A. T., Mawejje, H. D., Tomlinson, S., Rigden, D. J., & Donnelly, M. J. (2018). Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance. BMC GENOMICS, 19. doi:10.1186/s12864-018-4605-1
Autophosphorylation is a mechanism of inhibition in twitchin kinase
Williams, R., Franke, B., Wilkinson, M., Fleming, J., Rigden, D. J., Benian, G., . . . Mayans, O. (2018). Autophosphorylation is a mechanism of inhibition in twitchin kinase. Journal of Molecular Biology, 430(6), 793-805. doi:10.1016/j.jmb.2018.01.020
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in <i>AMPLE</i>
Rigden, D. J., Thomas, J. M. H., Simkovic, F., Simpkin, A., Winn, M. D., Mayans, O., & Keegan, R. M. (2018). Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in <i>AMPLE</i>. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 74, 183-193. doi:10.1107/S2059798318002310
Recent developments in <i>MrBUMP</i>: better search-model preparation, graphical interaction with search models, and solution improvement and assessment
Keegan, R. M., McNicholas, S. J., Thomas, J. M. H., Simpkin, A. J., Simkovic, F., Uski, V., . . . Rigden, D. J. (2018). Recent developments in <i>MrBUMP</i>: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 74, 167-182. doi:10.1107/S2059798318003455
Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae
Weetman, D., Wilding, C., Neafsey, D., Muller, P., Ochomo, E., Isaacs, A., . . . Donnelly, M. (2018). Candidate-gene based GWAS identifies reproducible DNA markers for metabolic pyrethroid resistance from standing genetic variation in East African Anopheles gambiae. Scientific Reports, 8. doi:10.1038/s41598-018-21265-5
The 2018 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection
Rigden, D. J., & Fernandez, X. M. (2018). The 2018 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 46(D1), D1-D7. doi:10.1093/nar/gkx1235
Covariation-derived residue contacts in template-free modelling and Molecular Replacement
Šimkovic, F. (2018). Covariation-derived residue contacts in template-free modelling and Molecular Replacement.
Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of <i>Trypanosoma cruzi</i>
Rojas-Pirela, M., Rigden, D. J., Michels, P. A., Caceres, A. J., Concepcion, J. L., & Quinones, W. (2018). Structure and function of Per-ARNT-Sim domains and their possible role in the life-cycle biology of <i>Trypanosoma cruzi</i>. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 219, 52-66. doi:10.1016/j.molbiopara.2017.11.002
2017
Approaches to ab initio molecular replacement of α-helical transmembrane proteins
Thomas, J. M. H., Simkovic, F., Keegan, R., Mayans, O., Zhang, C., Zhang, Y., & Rigden, D. J. (2017). Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallographica Section D: Structural Biology, 73(12), 985-996. doi:10.1107/S2059798317016436
SIMBAD: A Sequence-independent molecular replacement pipeline
Simpkin, A. J., Lebedev, A., Uski, V., Ballard, C., Shepard, W., Rigden, D., & Keegan, R. (2017). SIMBAD: A Sequence-independent molecular replacement pipeline. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 73 (pp. C1004). doi:10.1107/S2053273317085709
SIMBAD: A Sequence-independent molecular replacement pipeline
Simpkin, A. J., Lebedev, A., Uski, V., Ballard, C., Shepard, W., Rigden, D., & Keegan, R. (2014). SIMBAD: A Sequence-independent molecular replacement pipeline. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 70 (pp. C1004). Retrieved from http://gateway.webofknowledge.com/
Unconventional molecular replacement for helical transmembrane proteins using AMPLE
Simkovic, F., Thomas, J., Mayans, O., & Rigden, D. (2014). Unconventional molecular replacement for helical transmembrane proteins using AMPLE. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 70 (pp. C882). Retrieved from http://gateway.webofknowledge.com/
Unconventional molecular replacement for helical transmembrane proteins using AMPLE
Simkovic, F., Thomas, J., Mayans, O., & Rigden, D. (2017). Unconventional molecular replacement for helical transmembrane proteins using AMPLE. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 73 (pp. C882). doi:10.1107/S2053273317086922
Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus
Loxley, G. M., Unsworth, J., Turton, M. J., Jebb, A., Lilley, K. S., Simpson, D. M., . . . Beynon, R. J. (2017). Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus. Open Biology, 7(9). doi:10.1098/rsob.170135
Novel compound heterozygous <i>ASXL3</i> mutation causing Bainbridge-ropers like syndrome and primary IGF1 deficiency
Giri, D., Rigden, D., Didi, M., Peak, M., McNamara, P., & Senniappan, S. (2017). Novel compound heterozygous <i>ASXL3</i> mutation causing Bainbridge-ropers like syndrome and primary IGF1 deficiency. INTERNATIONAL JOURNAL OF PEDIATRIC ENDOCRINOLOGY. doi:10.1186/s13633-017-0047-9
ConKit: a python interface to contact predictions
Simkovic, F., Thomas, J. M. H., & Rigden, D. J. (2017). ConKit: a python interface to contact predictions. BIOINFORMATICS, 33(14), 2209-2211. doi:10.1093/bioinformatics/btx148
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.
Galperin, M. Y., Fernandez-Suarez, X. M., & Rigden, D. J. (2017). The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes (vol 45, pg D1, 2017). NUCLEIC ACIDS RESEARCH, 45(9), 5627. doi:10.1093/nar/gkx021
Applications of contact predictions to structural biology
Simkovic, F., Oychinnikov, S., Baker, D., & Rigden, D. J. (2017). Applications of contact predictions to structural biology. IUCRJ, 4, 291-300. doi:10.1107/S2052252517005115
From Protein Structure to Function with Bioinformatics
Rigden, D. (Ed.) (2009). From Protein Structure to Function with Bioinformatics. Dordrecht: Springer.
From Protein Structure to Function with Bioinformatics
J. Rigden, D. (Ed.) (2017). From Protein Structure to Function with Bioinformatics. Springer Netherlands. doi:10.1007/978-94-024-1069-3
Function Prediction Using Patches, Pockets and Other Surface Properties
Rigden, D. J. (2017). Function Prediction Using Patches, Pockets and Other Surface Properties. In From Protein Structure to Function with Bioinformatics (pp. 327-360). Springer Netherlands. doi:10.1007/978-94-024-1069-3_10
Prediction of Protein Function from Theoretical Models
Rigden, D. J., Cymerman, I. A., & Bujnicki, J. M. (2017). Prediction of Protein Function from Theoretical Models. In From Protein Structure to Function with Bioinformatics (pp. 467-498). Springer Netherlands. doi:10.1007/978-94-024-1069-3_15
Genome-Wide Association Study of Nevirapine Hypersensitivity in a sub-Saharan African HIV-infected Population
Carr, D. F., Bourgeois, S., Chaponda, M., Takeshita, L., Morris, A., Cornejo Castro, E. M., . . . Pirmohamed, M. (2017). Genome-Wide Association Study of Nevirapine Hypersensitivity in a sub-Saharan African HIV-infected Population. Journal of Antimicrobial Chemotherapy, 72(4), 1152-1162. doi:10.1093/jac/dkw545
Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics
Davies, H. A., Rigden, D. J., Phelan, M. M., & Madine, J. (2017). Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics. Scientific Reports, 7. doi:10.1038/srep45224
2016
The centrosomal Deubiquitylase USP21 regulates Gli1 transcriptional activity and stability
Heride, C., Rigden, D. J., Bertsoulaki, E., Cucchi, D., De Smaele, E., Clague, M. J., & Urbe, S. (2016). The centrosomal Deubiquitylase USP21 regulates Gli1 transcriptional activity and stability. Journal of Cell Science, 129(21), 4001-4013. doi:10.1242/jcs.188516
Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold
Zacharchenko, T., Barsukov, I., Rigden, D. J., Bennett, D., & Mayans, O. (2016). Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold. Protein Journal, 35(5), 240-345. doi:10.1007/s10930-016-9677-7
Potential DNA binding and nuclease functions of ComEC domains characterised in silico
Baker, J. A., Simkovic, F., Taylor, H. M. C., & Rigden, D. J. (2016). Potential DNA binding and nuclease functions of ComEC domains characterised in silico. Proteins: Structure, Function, and Bioinformatics, 84, 1431-1442. doi:10.1002/prot.25088
CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex
Zhou, T., Fleming, J. R., Franke, B., Bogomolovas, J., Barsukov, I., Rigden, D. J., . . . Mayans, O. (2016). CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex. FEBS LETTERS, 590(18), 3098-3110. doi:10.1002/1873-3468.12362
Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I
Bogomolovas, J., Fleming, J. R., Anderson, B. R., Williams, R., Lange, S., Simon, B., . . . Mayans, O. (2016). Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I. Open Biology, 6(9). doi:10.1098/rsob.160114
Combining unconventional MR with AMPLE <i>ab initio</i> models and experimental phasing
Simpkin, A. J., Mayans, O., Rigden, D. J., Savko, M., Shepard, W. E., & Keegan, R. (2016). Combining unconventional MR with AMPLE <i>ab initio</i> models and experimental phasing. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 72 (pp. S200). doi:10.1107/S2053273316096996
Current and future potential of contact predictions for X-ray crystallography
Simkovic, F., Thomas, J. M. H., Mayans, O., & Rigden, D. J. (2016). Current and future potential of contact predictions for X-ray crystallography. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 72 (pp. S200). doi:10.1107/S205327331609700X
Unconventional Molecular Replacement approaches for ab initio phasing of transmembrane helical protein targets
Thomas, J. M. H., Simkovic, F., Keegan, R. M., Mayans, O., & Rigden, D. J. (2016). Unconventional Molecular Replacement approaches for ab initio phasing of transmembrane helical protein targets. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 72 (pp. S224). doi:10.1107/S2053273316096595
GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ.
Simpkin, A. J., & Rigden, D. J. (2016). GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ.. BMC research notes, 9, 343. doi:10.1186/s13104-016-2149-5
Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds
Simkovic, F., Thomas, J., Keegan, R. M., Winn, M. D., Mayans, O., & Rigden, D. J. (2016). Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCrJ, 3(4), 259-270. doi:10.1107/S2052252516008113
The industrial melanism mutation in British peppered moths is a transposable element
Hof, A. E. V. T., Campagne, P., Rigden, D. J., Yung, C. J., Lingley, J., Quail, M. A., . . . Saccheri, I. J. (2016). The industrial melanism mutation in British peppered moths is a transposable element. Nature, 534(7605), 102-105. doi:10.1038/nature17951
The 2016 database issue of <i>Nucleic Acids</i> <i>Research</i> and an updated molecular biology database collection
Rigden, D. J., Fernandez-Suarez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of <i>Nucleic Acids</i> <i>Research</i> and an updated molecular biology database collection. NUCLEIC ACIDS RESEARCH, 44(D1), D1-D6. doi:10.1093/nar/gkv1356
Role of peptidoglycan deacetylase in Staphylococcus aureus virulence and survival
Alorabi, J. A. (2016). Role of peptidoglycan deacetylase in Staphylococcus aureus virulence and survival.
Structural and biochemical characterisation of the regulatory principles of twitchin kinase, a member of the titin-like family of muscle kinases
Williams, R. M. (2016). Structural and biochemical characterisation of the regulatory principles of twitchin kinase, a member of the titin-like family of muscle kinases.
2015
Structural advances on titin: towards an atomic understanding of multi-domain functions in myofilament mechanics and scaffolding
Zacharchenko, T., von Castelmur, E., Rigden, D. J., & Mayans, O. (2015). Structural advances on titin: towards an atomic understanding of multi-domain functions in myofilament mechanics and scaffolding. BIOCHEMICAL SOCIETY TRANSACTIONS, 43, 850-855. doi:10.1042/BST20150084
AMPLE: exploiting structural bioinformatics developments to extend the reach of molecular replacement to difficult cases
Rigden, D., Thomas, J., Keegan, R., Simkovic, F., Winn, M., & Mayans, O. (2015). AMPLE: exploiting structural bioinformatics developments to extend the reach of molecular replacement to difficult cases. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 71 (pp. S42). doi:10.1107/S2053273315099349
ATG24 Represses Autophagy and Differentiation and Is Essential for Homeostasy of the Flagellar Pocket in <i>Trypanosoma brucei</i>
Brennand, A., Rico, E., Rigden, D. J., Van Der Smissen, P., Courtoy, P. J., & Michels, P. A. M. (2015). ATG24 Represses Autophagy and Differentiation and Is Essential for Homeostasy of the Flagellar Pocket in <i>Trypanosoma brucei</i>. PLOS ONE, 10(6). doi:10.1371/journal.pone.0130365
Contemporary evolution of resistance at the major insecticide target site gene <i>Ace-1</i> by mutation and copy number variation in the malaria mosquito <i>Anophelesgambiae</i>
Weetman, D., Mitchell, S. N., Wilding, C. S., Birks, D. P., Yawson, A. E., Essandoh, J., . . . Donnelly, M. J. (2015). Contemporary evolution of resistance at the major insecticide target site gene <i>Ace-1</i> by mutation and copy number variation in the malaria mosquito <i>Anophelesgambiae</i>. MOLECULAR ECOLOGY, 24(11), 2656-2672. doi:10.1111/mec.13197
Lpg0393 of Legionella pneumophila is a guanine-nucleotide exchange factor for Rab5, Rab21 and Rab22
Sohn, Y. -S., Shin, H. -C., Park, W. S., Ge, J., Kim, C. H., Bok, L. L., . . . Oh, B. H. (2015). Lpg0393 of Legionella pneumophila is a guanine-nucleotide exchange factor for Rab5, Rab21 and Rab22. PLoS ONE, 10(3). doi:10.1371/journal.pone.0118683
Routine phasing of coiled-coil protein crystal structures with <i>AMPLE</i>
Thomas, J. M. H., Keegan, R. M., Bibby, J., Winn, M. D., Mayans, O., & Rigden, D. J. (2015). Routine phasing of coiled-coil protein crystal structures with <i>AMPLE</i>. IUCRJ, 2, 198-206. doi:10.1107/S2052252515002080
Exploring the speed and performance of molecular replacement with <i>AMPLE</i> using <i>QUARK ab initio</i> protein models
Keegan, R. M., Bibby, J., Thomas, J., Xu, D., Zhang, Y., Mayans, O., . . . Rigden, D. J. (2015). Exploring the speed and performance of molecular replacement with <i>AMPLE</i> using <i>QUARK ab initio</i> protein models. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 71, 338-343. doi:10.1107/S1399004714025784
The 2015 <i>Nucleic Acids Research</i> Database Issue and Molecular Biology Database Collection
Galperin, M. Y., Rigden, D. J., & Fernandez-Suarez, X. M. (2015). The 2015 <i>Nucleic Acids Research</i> Database Issue and Molecular Biology Database Collection. NUCLEIC ACIDS RESEARCH, 43(D1), D1-D5. doi:10.1093/nar/gku1241
Transcriptomic Analysis of Shiga-Toxigenic Bacteriophage Carriage Reveals a Profound Regulatory Effect on Acid Resistance in Escherichia coli
Veses-Garcia, M., Liu, X., Rigden, D. J., Kenny, J. G., McCarthy, A. J., & Allison, H. E. (2015). Transcriptomic Analysis of Shiga-Toxigenic Bacteriophage Carriage Reveals a Profound Regulatory Effect on Acid Resistance in Escherichia coli. Applied and Environmental Microbiology, 81(23), 8118-8125. doi:10.1128/AEM.02034-15
2014
Extracellular calcium triggers unique transcriptional programs and modulates staurosporine-induced cell death in <i>Neurospora crassa</i>.
Gonçalves, A. P., Monteiro, J., Lucchi, C., Kowbel, D. J., Cordeiro, J. M., Correia-de-Sá, P., . . . Videira, A. (2014). Extracellular calcium triggers unique transcriptional programs and modulates staurosporine-induced cell death in <i>Neurospora crassa</i>.. Microbial cell (Graz, Austria), 1(9), 289-302. doi:10.15698/mic2014.09.165
Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE
Thomas, J., Keegan, R., Bibby, J., Winn, M., Mayans, O., & Rigden, D. (2014). Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 70, C347. doi:10.1107/S2053273314096521
Evidence for Loss of a Partial Flagellar Glycolytic Pathway during Trypanosomatid Evolution
Brown, R. W. B., Collingridge, P. W., Gull, K., Rigden, D. J., & Ginger, M. L. (2014). Evidence for Loss of a Partial Flagellar Glycolytic Pathway during Trypanosomatid Evolution. PLOS ONE, 9(7). doi:10.1371/journal.pone.0103026
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase
Rigden, D. J., Eberhardt, R. Y., Gilbert, H. J., Xu, Q., Chang, Y., & Godzik, A. (2014). Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. BMC Bioinformatics, 15. doi:10.1186/1471-2105-15-196
Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line
Bogomolovas, J., Gasch, A., Simkovic, F., Rigden, D. J., Labeit, S., & Mayans, O. (2014). Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line. Open Biology, 4. doi:10.1098/rsob.140041
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase
Sheydina, A., Eberhardt, R. Y., Rigden, D. J., Chang, Y., Li, Z., Zmasek, C., . . . Godzik, A. (2014). Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. BMC Bioinformatics, 15. doi:10.1186/1471-2105-15-112
<i>AMPLE</i>: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed <i>ab initio</i> models (vol 68, pg 1622, 2012)
Bibby, J., Keegan, R. M., Mayans, O., Winn, M. D., & Rigden, D. J. (2014). <i>AMPLE</i>: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed <i>ab initio</i> models (vol 68, pg 1622, 2012). ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70, 1174. doi:10.1107/S1399004714006154
Metabolic and Target-Site Mechanisms Combine to Confer Strong DDT Resistance in <i>Anopheles gambiae</i>
Mitchell, S. N., Rigden, D. J., Dowd, A. J., Lu, F., Wilding, C. S., Weetman, D., . . . Donnelly, M. J. (2014). Metabolic and Target-Site Mechanisms Combine to Confer Strong DDT Resistance in <i>Anopheles gambiae</i>. PLOS ONE, 9(3). doi:10.1371/journal.pone.0092662
Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1
Franke, B., Gasch, A., Rodriguez, D., Chami, M., Khan, M. M., Rudolf, R., . . . Mayans, O. (2014). Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1. Open Biology, 4(3). doi:10.1098/rsob.130172
Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis
Hotta, K., Keegan, R. M., Ranganathan, S., Fang, M., Bibby, J., Winn, M. D., . . . Kim, C. (2014). Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis. Angewandte Chemie, 126(3), 843-847. doi:10.1002/ange.201307404
Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis
Hotta, K., Keegan, R. M., Ranganathan, S., Fang, M., Bibby, J., Winn, M. D., . . . Kim, C. -Y. (2014). Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis. Angewandte Chemie International Edition, 53(3), 824-828. doi:10.1002/anie.201307404
Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain
Bruhn, J. F., Barnett, K. C., Bibby, J., Thomas, J. M. H., Keegan, R. M., Rigden, D. J., . . . Saphire, E. O. (2014). Crystal Structure of the Nipah Virus Phosphoprotein Tetramerization Domain. JOURNAL OF VIROLOGY, 88(1), 758-762. doi:10.1128/JVI.02294-13
Structural basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1
Franke, B., Gasch, A., Rodriguez, D., Chami, M., Khan, M. M., Rudolf, R., . . . Mayans, O. (2014). Structural basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1. Open Biology, 4, 130172.
The 2014 <i>Nucleic Acids Research</i> Database Issue and an updated NAR online Molecular Biology Database Collection
Fernandez-Suarez, X. M., Rigden, D. J., & Galperin, M. Y. (2014). The 2014 <i>Nucleic Acids Research</i> Database Issue and an updated NAR online Molecular Biology Database Collection. NUCLEIC ACIDS RESEARCH, 42(D1), D1-D6. doi:10.1093/nar/gkt1282
2013
Ubiquitination of the glycosomal matrix protein receptor PEX5 in <i>Trypanosoma brucei</i> by PEX4 displays novel features
Gualdron-Lopez, M., Chevalier, N., Van der Smissen, P., Courtoy, P. J., Rigden, D. J., & Michels, P. A. M. (2013). Ubiquitination of the glycosomal matrix protein receptor PEX5 in <i>Trypanosoma brucei</i> by PEX4 displays novel features. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 1833(12), 3076-3092. doi:10.1016/j.bbamcr.2013.08.008
Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement
Bibby, J., Keegan, R. M., Mayans, O., Winn, M. D., & Rigden, D. J. (2013). Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 69, 2194-2201. doi:10.1107/S0907444913018453
Employing <i>in vitro</i> directed molecular evolution for the selection of α-amylase variant inhibitors with activity toward cotton boll weevil enzyme
Mattar da Silva, M. C., Del Sarto, R. P., Lucena, W. A., Rigden, D. J., Teixeira, F. R., Bezerra, C. D. A., . . . Grossi-de-sa, M. F. (2013). Employing <i>in vitro</i> directed molecular evolution for the selection of α-amylase variant inhibitors with activity toward cotton boll weevil enzyme. JOURNAL OF BIOTECHNOLOGY, 167(4), 377-385. doi:10.1016/j.jbiotec.2013.07.016
<i>AMPLE</i>- using<i>de novo</i>protein structure modelling techniques to create and enhance search models for use in molecular replacement
Keegan, R., Bibby, J., Thomas, J., Rigden, D., & Winn, M. (2013). <i>AMPLE</i>- using<i>de novo</i>protein structure modelling techniques to create and enhance search models for use in molecular replacement. Acta Crystallographica Section A Foundations of Crystallography, 69(a1), s298. doi:10.1107/s0108767313097420
<i>AMPLE</i>– using<i>de novo</i>protein structure modelling techniques to create and enhance search models for use in molecular replacement
Keegan, R., Bibby, J., Thomas, J., Rigden, D., & Winn, M. (2013). <i>AMPLE</i>– using<i>de novo</i>protein structure modelling techniques to create and enhance search models for use in molecular replacement. Acta Crystallographica Section A Foundations of Crystallography, 69(a1), s44. doi:10.1107/s0108767313099613
The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold.
Rigden, D. J., Xu, Q., Chang, Y., Eberhardt, R. Y., Finn, R. D., & Rawlings, N. D. (2013). The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold.. F1000Research, 2, 154. doi:10.12688/f1000research.2-154.v2
Mechanistic and functional diversity in the mechanosensory kinases of the titin-like family
Mayans, O., Benian, G. M., Simkovic, F., & Rigden, D. J. (2013). Mechanistic and functional diversity in the mechanosensory kinases of the titin-like family. BIOCHEMICAL SOCIETY TRANSACTIONS, 41, 1066-1071. doi:10.1042/BST20130085
The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold
Rigden, D. J., Xu, Q., Chang, Y., Eberhardt, R. Y., Finn, R. D., & Rawlings, N. D. (n.d.). The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold. F1000Research, 2, 154. doi:10.12688/f1000research.2-154.v1
DEUBIQUITYLASES FROM GENES TO ORGANISM
Clague, M. J., Barsukov, I., Coulson, J. M., Liu, H., Rigden, D. J., & Urbe, S. (2013). DEUBIQUITYLASES FROM GENES TO ORGANISM. PHYSIOLOGICAL REVIEWS, 93(3), 1289-1315. doi:10.1152/physrev.00002.2013
Deubiquitylases From Genes to Organism
Clague, M. J., Barsukov, I., Coulson, J. M., Liu, H., Rigden, D. J., & Urbé, S. (2013). Deubiquitylases From Genes to Organism. Physiological Reviews, 93(3), 1289-1315. doi:10.1152/physrev.00002.2013
Correction: Evaluating Caveolin Interactions: Do Proteins Interact with the Caveolin Scaffolding Domain through a Widespread Aromatic Residue-Rich Motif?
Byrne, D. P., Dart, C., & Rigden, D. J. (2013). Correction: Evaluating Caveolin Interactions: Do Proteins Interact with the Caveolin Scaffolding Domain through a Widespread Aromatic Residue-Rich Motif?. PloS one, 8(2). doi:10.1371/annotation/2c275a1b-2d36-4492-b36a-192bddf14f78
Genome of <i>Acanthamoeba castellanii</i> highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling
Clarke, M., Lohan, A. J., Liu, B., Lagkouvardos, I., Roy, S., Zafar, N., . . . Loftus, B. J. (2013). Genome of <i>Acanthamoeba castellanii</i> highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. GENOME BIOLOGY, 14(2). doi:10.1186/gb-2013-14-2-r11
Mechanistic and functional diversity in the mechanosensory kinases of the titin-like family
Mayans, O., Benian, G. M., Simkovic, F., & Rigden, D. J. (2013). Mechanistic and functional diversity in the mechanosensory kinases of the titin-like family. Biochem Soc Trans, 41, 1066-1071.
2012
<i>AMPLE</i>: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed <i>ab initio</i> models
Bibby, J., Keegan, R. M., Mayans, O., Winn, M. D., & Rigden, D. J. (2012). <i>AMPLE</i>: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed <i>ab initio</i> models. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 68, 1622-1631. doi:10.1107/S0907444912039194
A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods
Mello, L. V., & Rigden, D. J. (2012). A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods. FEBS LETTERS, 586(21), 3908-3913. doi:10.1016/j.febslet.2012.09.023
Genomic determinants of sporulation in <i>Bacilli</i> and <i>Clostridia</i>: towards the minimal set of sporulation-specific genes
Galperin, M. Y., Mekhedov, S. L., Puigbo, P., Smirnov, S., Wolf, Y. I., & Rigden, D. J. (2012). Genomic determinants of sporulation in <i>Bacilli</i> and <i>Clostridia</i>: towards the minimal set of sporulation-specific genes. ENVIRONMENTAL MICROBIOLOGY, 14(11), 2870-2890. doi:10.1111/j.1462-2920.2012.02841.x
Evaluating Caveolin Interactions: Do Proteins Interact with the Caveolin Scaffolding Domain through a Widespread Aromatic Residue-Rich Motif?
Byrne, D. P., Dart, C., & Rigden, D. J. (2012). Evaluating Caveolin Interactions: Do Proteins Interact with the Caveolin Scaffolding Domain through a Widespread Aromatic Residue-Rich Motif?. PLOS ONE, 7(9). doi:10.1371/journal.pone.0044879
A cluster and truncate approach to processing<i>ab initio</i>models for molecular replacement
Rigden, D., Bibby, J., Mayans, O., Keegan, R., & Winn, M. (2012). A cluster and truncate approach to processing<i>ab initio</i>models for molecular replacement. Acta Crystallographica Section A Foundations of Crystallography, 68(a1), s121. doi:10.1107/s0108767312097644
mRNA 3′ Tagging Is Induced by Nonsense-Mediated Decay and Promotes Ribosome Dissociation
Morozov, I. Y., Jones, M. G., Gould, P. D., Crome, V., Wilson, J. B., Hall, A. J. W., . . . Caddick, M. X. (2012). mRNA 3′ Tagging Is Induced by Nonsense-Mediated Decay and Promotes Ribosome Dissociation. MOLECULAR AND CELLULAR BIOLOGY, 32(13), 2585-2595. doi:10.1128/MCB.00316-12
Trypanosomes contain two highly different isoforms of peroxin PEX13 involved in glycosome biogenesis
Brennand, A., Rigden, D. J., & Michels, P. A. M. (2012). Trypanosomes contain two highly different isoforms of peroxin PEX13 involved in glycosome biogenesis. FEBS LETTERS, 586(13), 1765-1771. doi:10.1016/j.febslet.2012.05.019
Rab14 and Its Exchange Factor FAM116 Link Endocytic Recycling and Adherens Junction Stability in Migrating Cells
Linford, A., Yoshimura, S. -I., Bastos, R. N., Langemeyer, L., Gerondopoulos, A., Rigden, D. J., & Barr, F. A. (2012). Rab14 and Its Exchange Factor FAM116 Link Endocytic Recycling and Adherens Junction Stability in Migrating Cells. DEVELOPMENTAL CELL, 22(5), 952-966. doi:10.1016/j.devcel.2012.04.010
Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions
Urbé, S., Liu, H., Hayes, S. D., Heride, C., Rigden, D. J., & Clague, M. J. (2012). Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions. Molecular Biology of the Cell, 23(6), 1095-1103. doi:10.1091/mbc.e11-08-0668
Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions
Urbe, S., Liu, H., Hayes, S. D., Heride, C., Rigden, D. J., & Clague, M. J. (2012). Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions. MOLECULAR BIOLOGY OF THE CELL, 23(6), 1095-1103. doi:10.1091/mbc.E11-08-0668
Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster
Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster (2012). PloS one, 7(1).
Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster
Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster (2012). PloS one, 7(1).
Genomic determinants of sporulation: A minimal set of sporulation-specific genes in Bacilli and Clostridia
Galperin, M. Y., Mekhedov, S. L., Puigbo, P., Smirnov, S., Wolf, Y. I., & Rigden, D. J. (2012). Genomic determinants of sporulation: A minimal set of sporulation-specific genes in Bacilli and Clostridia. Environmental Microbiology, 14, 2870-2890.
Prediction of antimicrobial peptides based on the adaptive neuro-fuzzy inference system application
Fernandes, F. C., Rigden, D. J., & Franco, O. L. (2012). Prediction of antimicrobial peptides based on the adaptive neuro-fuzzy inference system application. BIOPOLYMERS, 98(4), 280-287. doi:10.1002/bip.22066
Rational Prediction of Antimicrobial Peptides Based on the Adaptive Neuro-Fuzzy Inference System (ANFIS) Application
Fernandes, F. C., Rigden, D. J., & Franco, O. L. (2012). Rational Prediction of Antimicrobial Peptides Based on the Adaptive Neuro-Fuzzy Inference System (ANFIS) Application. Biopolymers, 98, 280-287.
2011
Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster
Ayres, C., Mueller, P., Dyer, N., Wilding, C., Rigden, D., & Donnelly, M. (2011). Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster. PLOS ONE, 6(12). doi:10.1371/journal.pone.0029237
Structural variability of the ubiquitin specific protease DUSP-UBL double domains
Elliott, P. R., Liu, H., Pastok, M. W., Grossmann, G. J., Rigden, D. J., Clague, M. J., . . . Barsukov, I. L. (2011). Structural variability of the ubiquitin specific protease DUSP-UBL double domains. FEBS LETTERS, 585(21), 3385-3390. doi:10.1016/j.febslet.2011.09.040
Improving Cry8Ka toxin activity towards the cotton boll weevil (<i>Anthonomus grandis</i>)
Oliveira, G. R., Silva, M. C. M., Lucena, W. A., Nakasu, E. Y. T., Firmino, A. A. P., Beneventi, M. A., . . . Grossi-de-Sa, M. F. (2011). Improving Cry8Ka toxin activity towards the cotton boll weevil (<i>Anthonomus grandis</i>). BMC BIOTECHNOLOGY, 11. doi:10.1186/1472-6750-11-85
Identification and modelling of a PPM protein phosphatase fold in the <i>Legionella pneumophila</i> deAMPylase SidD
Rigden, D. J. (2011). Identification and modelling of a PPM protein phosphatase fold in the <i>Legionella pneumophila</i> deAMPylase SidD. FEBS LETTERS, 585(17), 2749-2754. doi:10.1016/j.febslet.2011.08.006
Structure solution by molecular replacement using<i>ab initio</i>protein models
Rigden, D., Bibby, J., Mayans, O., Keegan, R., & Winn, M. (2011). Structure solution by molecular replacement using<i>ab initio</i>protein models. Acta Crystallographica Section A Foundations of Crystallography, 67(a1), C134-C135. doi:10.1107/s0108767311096693
<i>Ab Initio</i> Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs
Rigden, D. J. (2011). <i>Ab Initio</i> Modeling Led Annotation Suggests Nucleic Acid Binding Function for Many DUFs. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 15(7-8), 431-438. doi:10.1089/omi.2010.0122
Characterisation of a Desmosterol Reductase Involved in Phytosterol Dealkylation in the Silkworm, <i>Bombyx mori</i>
Ciufo, L. F., Murray, P. A., Thompson, A., Rigden, D. J., & Rees, H. H. (2011). Characterisation of a Desmosterol Reductase Involved in Phytosterol Dealkylation in the Silkworm, <i>Bombyx mori</i>. PLOS ONE, 6(6). doi:10.1371/journal.pone.0021316
New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins
Rigden, D. J., Woodhead, D. D., Wong, P. W. H., & Galperin, M. Y. (2011). New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins. PLOS ONE, 6(6). doi:10.1371/journal.pone.0021507
Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage
Fogg, P. C. M., Rigden, D. J., Saunders, J. R., McCarthy, A. J., & Allison, H. E. (2011). Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage. NUCLEIC ACIDS RESEARCH, 39(6), 2116-2129. doi:10.1093/nar/gkq923
Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR
Ferraz, L. F. C., Verde, L. C. L., Vicentini, R., Felicio, A. P., Ribeiro, M. L., Alexandrino, F., . . . Ottoboni, L. M. M. (2011). Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR. ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, 99(3), 609-617. doi:10.1007/s10482-010-9533-2
Autophagy in parasitic protists: Unique features and drug targets
Brennand, A., Gualdron-Lopez, M., Coppens, I., Rigden, D. J., Ginger, M. L., & Michels, P. A. M. (2011). Autophagy in parasitic protists: Unique features and drug targets. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 177(2), 83-99. doi:10.1016/j.molbiopara.2011.02.003
Autophagy in protists
Duszenko, M., Ginger, M. L., Brennand, A., Gualdron-Lopez, M., Colombo, M. -I., Coombs, G. H., . . . Michels, P. A. M. (2011). Autophagy in protists. AUTOPHAGY, 7(2), 127-158. doi:10.4161/auto.7.2.13310
Characterisation of a Desmosterol Reductase Involved in Phytosterol Dealkylation in the Silkworm, Bombyx mori
Ciufo, L. F., Murray, P. A., Thompson, A., Rigden, D. J., & Rees, H. H. (n.d.). Characterisation of a Desmosterol Reductase Involved in Phytosterol Dealkylation in the Silkworm, Bombyx mori. PLoS ONE, 6(6), e21316. doi:10.1371/journal.pone.0021316
2010
Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors
Yoshimura, S. -I., Gerondopoulos, A., Linford, A., Rigden, D. J., & Barr, F. A. (2010). Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. JOURNAL OF CELL BIOLOGY, 191(2), 367-381. doi:10.1083/jcb.201008051
Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module
Mello, L. V., Chen, X., & Rigden, D. J. (2010). Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module. FEBS LETTERS, 584(11), 2421-2426. doi:10.1016/j.febslet.2010.04.045
Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation
Polson, H. E. J., de lartigue, J., Rigden, D. J., Reedijk, M., Urbe, S., Clague, M. J., & Tooze, S. A. (2010). Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. AUTOPHAGY, 6(4), 506-522. doi:10.4161/auto.6.4.11863
CUCU Modification of mRNA Promotes Decapping and Transcript Degradation in <i>Aspergillus nidulans</i>
Morozov, I. Y., Jones, M. G., Razak, A. A., Rigden, D. J., & Caddick, M. X. (2010). CUCU Modification of mRNA Promotes Decapping and Transcript Degradation in <i>Aspergillus nidulans</i>. MOLECULAR AND CELLULAR BIOLOGY, 30(2), 460-469. doi:10.1128/MCB.00997-09
Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in <i>Aspergillus nidulans</i>
Morozov, I. Y., Jones, M. G., Spiller, D. G., Rigden, D. J., Dattenboeck, C., Novotny, R., . . . Caddick, M. X. (2010). Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in <i>Aspergillus nidulans</i>. MOLECULAR MICROBIOLOGY, 76(2), 503-516. doi:10.1111/j.1365-2958.2010.07118.x
Intracellular Delivery and Fate of Peptide-Capped Gold Nanoparticles
Cesbron, Y., See, V., Free, P., Nativo, P., Shaheen, U., Rigden, D. J., . . . Levy, R. (2010). Intracellular Delivery and Fate of Peptide-Capped Gold Nanoparticles. In BIOPHYSICAL JOURNAL Vol. 98 (pp. 203A). doi:10.1016/j.bpj.2009.12.1081
2009
Identification of novel aspartic proteases from <i>Strongyloides ratti</i> and characterisation of their evolutionary relationships, stage-specific expression and molecular structure
Mello, L. V., O'Meara, H., Rigden, D. J., & Paterson, S. (2009). Identification of novel aspartic proteases from <i>Strongyloides ratti</i> and characterisation of their evolutionary relationships, stage-specific expression and molecular structure. BMC GENOMICS, 10. doi:10.1186/1471-2164-10-611
From Protein Structure to Function with Bioinformatics
Rigden, D. J. (Ed.) (2009). From Protein Structure to Function with Bioinformatics. Springer Netherlands. doi:10.1007/978-1-4020-9058-5
Cathepsin L Digestion of Nanobioconjugates upon Endocytosis
See, V., Free, P., Cesbron, Y., Nativo, P., Shaheen, U., Rigden, D. J., . . . Levy, R. (2009). Cathepsin L Digestion of Nanobioconjugates upon Endocytosis. ACS NANO, 3(9), 2461-2468. doi:10.1021/nn9006994
Autophagy in protists Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion
Rigden, D. J., Michels, P. A., & Ginger, M. L. (2009). Autophagy in protists Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion. AUTOPHAGY, 5(6), 784-794. doi:10.4161/auto.8838
Molecular replacement using<i>ab initio</i>polyalanine models generated with<i>ROSETTA</i>
Winn, M., Rigden, D., & Keegan, R. (2009). Molecular replacement using<i>ab initio</i>polyalanine models generated with<i>ROSETTA</i>. Acta Crystallographica Section A Foundations of Crystallography, 65(a1), s163. doi:10.1107/s0108767309096664
Does distant homology with Evf reveal a lipid binding site in <i>Bacillus thuringiensis</i> cytolytic toxins?
Rigden, D. J. (2009). Does distant homology with Evf reveal a lipid binding site in <i>Bacillus thuringiensis</i> cytolytic toxins?. FEBS LETTERS, 583(10), 1555-1560. doi:10.1016/j.febslet.2009.04.038
Molecular Dynamics and Electrochemical Investigations of a pH-Responsive Peptide Monolayer
Doneux, T., Bouffier, L., Mello, L. V., Rigden, D. J., Kejnovska, I., Fernig, D. G., . . . Nichols, R. J. (2009). Molecular Dynamics and Electrochemical Investigations of a pH-Responsive Peptide Monolayer. JOURNAL OF PHYSICAL CHEMISTRY C, 113(16), 6792-6799. doi:10.1021/jp810859k
Ab initio protein modelling reveals novel human MIT domains
Rigden, D. J., Liu, H., Hayes, S. D., Urbe, S., & Clague, M. J. (2009). Ab initio protein modelling reveals novel human MIT domains. FEBS LETTERS, 583(5), 872-878. doi:10.1016/j.febslet.2009.02.012
Identification, characterization and essentiality of the unusual peroxin 13 from <i>Trypanosoma brucei</i>
Verplaetse, E., Rigden, D. J., & Michels, P. A. M. (2009). Identification, characterization and essentiality of the unusual peroxin 13 from <i>Trypanosoma brucei</i>. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 1793(3), 516-527. doi:10.1016/j.bbamcr.2008.12.020
Autophagy in protists - Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion
Rigden, D. J., Michels, P. A., & Ginger, M. L. (2009). Autophagy in protists - Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion. Autophagy, 5(6), 784-794.
2008
Molecular replacement using <i>ab initio</i> polyalanine models generated with <i>ROSETTA</i>
Rigden, D. J., Keegan, R. M., & Winn, M. D. (2008). Molecular replacement using <i>ab initio</i> polyalanine models generated with <i>ROSETTA</i>. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 64, 1288-1291. doi:10.1107/S0907444908033192
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium <i>Anoxybacillus flavithermus</i> WK1
Saw, J. H., Mountain, B. W., Feng, L., Omelchenko, M. V., Hou, S., Saito, J. A., . . . Alam, M. (2008). Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium <i>Anoxybacillus flavithermus</i> WK1. GENOME BIOLOGY, 9(11). doi:10.1186/gb-2008-9-11-r161
Sequence analysis of GerM and SpoVS, uncharacterized bacterial sporulation proteins with widespread phylogenetic distribution
Rigden, D. J., & Galperin, M. Y. (2008). Sequence analysis of GerM and SpoVS, uncharacterized bacterial sporulation proteins with widespread phylogenetic distribution. BIOINFORMATICS, 24(16), 1793-1797. doi:10.1093/bioinformatics/btn314
The histidine phosphatase superfamily: structure and function
Rigden, D. J. (2008). The histidine phosphatase superfamily: structure and function. BIOCHEMICAL JOURNAL, 409, 333-348. doi:10.1042/BJ20071097
Order within a mosaic distribution of mitochondrial <i>c</i>-type cytochrome biogenesis systems?
Allen, J. W. A., Jackson, A. P., Rigden, D. J., Willis, A. C., Ferguson, S. J., & Ginger, M. L. (2008). Order within a mosaic distribution of mitochondrial <i>c</i>-type cytochrome biogenesis systems?. FEBS JOURNAL, 275(10), 2385-2402. doi:10.1111/j.1742-4658.2008.06380.x
2007
Jaburetox-2Ec:: An insecticidal peptide derived from an isoform of urease from the plant <i>Canaualia ensiformis</i>
Mulinari, F., Staniscuaski, F., Bertholdo-Vargas, L. R., Postal, M., Oliveira-Neto, O. B., Riden, D. J., . . . Carlini, C. R. (2007). Jaburetox-2Ec:: An insecticidal peptide derived from an isoform of urease from the plant <i>Canaualia ensiformis</i>. PEPTIDES, 28(10), 2042-2050. doi:10.1016/j.peptides.2007.08.009
Structural flexibility in <i>Trypanosoma brucei</i> enolase revealed by X-ray crystallography and molecular dynamics
Navarro, M. V. D. A. S., Dias, S. M. G., Mello, L. V., Giotto, M. T. D. S., Gavalda, S., Blonski, C., . . . Rigden, D. J. (2007). Structural flexibility in <i>Trypanosoma brucei</i> enolase revealed by X-ray crystallography and molecular dynamics. FEBS JOURNAL, 274(19), 5077-5089. doi:10.1111/j.1742-4658.2007.06027.x
An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: Surprising relationship to insect ecdysteroid phosphate phosphatase
Davies, L., Anderson, I. P., Turner, P. C., Shirras, A. D., Rees, H. H., & Rigden, D. J. (2007). An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: Surprising relationship to insect ecdysteroid phosphate phosphatase. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 67(3), 720-731. doi:10.1002/prot.21357
The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase
Yu, Z., Genest, P. -A., ter Riet, B., Sweeney, K., DiPaolo, C., Kieft, R., . . . Borst, P. (2007). The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. NUCLEIC ACIDS RESEARCH, 35(7), 2107-2115. doi:10.1093/nar/gkm049
Genome-based identification and characterization of a putative mucin-binding protein from the surface of <i>Streptococcus pneumoniae</i>
Bumbaca, D., Littlejohn, J. E., Nayakanti, H., Lucas, A. H., Rigden, D. J., Galperin, M. Y., & Jedrzejas, M. J. (2007). Genome-based identification and characterization of a putative mucin-binding protein from the surface of <i>Streptococcus pneumoniae</i>. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66(3), 547-558. doi:10.1002/prot.21205
Acyl carrier protein phosphodiesterase (AcpH) of <i>Escherichia coli</i> is a non-canonical member of the HD phosphatase/phosphodiesterase family
Thomas, J., Rigden, D. J., & Cronan, J. E. (2007). Acyl carrier protein phosphodiesterase (AcpH) of <i>Escherichia coli</i> is a non-canonical member of the HD phosphatase/phosphodiesterase family. BIOCHEMISTRY, 46(1), 129-136. doi:10.1021/bi061789e
16th International Ecdysone Workshop: July 10–14, 2006, Ghent University, Belgium
16th International Ecdysone Workshop: July 10–14, 2006, Ghent University, Belgium (2007). Journal of insect science (Online), 7.
2006
Understanding the cell in terms of structure and function: insights from structural genomics
Rigden, D. J. (2006). Understanding the cell in terms of structure and function: insights from structural genomics. CURRENT OPINION IN BIOTECHNOLOGY, 17(5), 457-464. doi:10.1016/j.copbio.2006.07.004
Design of new benzoxazole-2-thione-derived inhibitors of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: structure of a complex with a 2-phenylindole
Rigden, D. J., Botzki, A., Nukui, M., Mewbourne, R. B., Lamani, E., Braun, S., . . . Jedrzejas, M. J. (2006). Design of new benzoxazole-2-thione-derived inhibitors of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: structure of a complex with a 2-phenylindole. GLYCOBIOLOGY, 16(8), 757-765. doi:10.1093/glycob/cwj116
Mutagenic definition of a papain-like catalytic triad, sufficiency of the N-terminal domain for single-site core catalytic enzyme acylation, and C-terminal domain for augmentative metal activation of a eukaryotic phytochelatin synthase
Romanyuk, N. D., Rigden, D. J., Vatamaniuk, O. K., Lang, A., Cahoon, R. E., Jez, J. M., & Rea, P. A. (2006). Mutagenic definition of a papain-like catalytic triad, sufficiency of the N-terminal domain for single-site core catalytic enzyme acylation, and C-terminal domain for augmentative metal activation of a eukaryotic phytochelatin synthase. PLANT PHYSIOLOGY, 141(3), 858-869. doi:10.1104/pp.106.082131
Molecular Modeling and inhibitory activity of cowpea cystatin against bean bruchid pests
Aguiar, J. M., Franco, O. L., Rigden, D. J., Bloch, C., Monteiro, A. C. S., Flores, V. M. Q., . . . Fernandes, K. V. S. (2006). Molecular Modeling and inhibitory activity of cowpea cystatin against bean bruchid pests. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63(3), 662-670. doi:10.1002/prot.20901
Alternate structural conformations of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: Insights into enzyme flexibility and underlying molecular mechanism of action
Rigden, D. J., Littlejohn, J. E., Joshi, H. V., de Groot, B. L., & Jedrzejas, M. J. (2006). Alternate structural conformations of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: Insights into enzyme flexibility and underlying molecular mechanism of action. JOURNAL OF MOLECULAR BIOLOGY, 358(4), 1165-1178. doi:10.1016/j.jmb.2006.02.066
Autophagy and related processes in trypanosomatids - Insights from genomic and bioinformatic analyses
Herman, M., Gillies, S., Michels, P. A., & Rigden, D. L. (2006). Autophagy and related processes in trypanosomatids - Insights from genomic and bioinformatic analyses. AUTOPHAGY, 2(2), 107-118. doi:10.4161/auto.2.2.2369
Evolutionary analysis of fructose 2,6-bisphosphate metabolism
Michels, P. A. M., & Rigden, D. J. (2006). Evolutionary analysis of fructose 2,6-bisphosphate metabolism. IUBMB LIFE, 58(3), 133-141. doi:10.1080/15216540600688280
2005
Implications of a genomic search for autophagy-related genes in trypanosomatids
Rigden, D. J., Herman, M., Gillies, S., & Michels, P. A. M. (2005). Implications of a genomic search for autophagy-related genes in trypanosomatids. BIOCHEMICAL SOCIETY TRANSACTIONS, 33, 972-974. doi:10.1042/BST0330972
Analysis of glycoside hydrolase family 98: Catalytic machinery, mechanism and a novel putative carbohydrate binding module
Rigden, D. J. (2005). Analysis of glycoside hydrolase family 98: Catalytic machinery, mechanism and a novel putative carbohydrate binding module. FEBS LETTERS, 579(25), 5466-5472. doi:10.1016/j.febslet.2005.09.011
Implications of a genomic search for autophagy-related genes in trypanosomatids.
Rigden, D. J., Herman, M., Gillies, S., & Michels, P. A. M. (2005). Implications of a genomic search for autophagy-related genes in trypanosomatids.. Biochemical Society transactions, 33(Pt 5), 972-974. doi:10.1042/bst20050972
Regulation of ecdysteroid signalling during <i>Drosophila</i> development:: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration
Takeuchi, H., Rigden, D. J., Ebrahimi, B., Turner, P. C., & Rees, H. H. (2005). Regulation of ecdysteroid signalling during <i>Drosophila</i> development:: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration. BIOCHEMICAL JOURNAL, 389, 637-645. doi:10.1042/BJ20050498
OMICS-related research in Latin America
Rigden, D. J., & Galperin, M. Y. (2005). OMICS-related research in Latin America. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 9(2), 129. doi:10.1089/omi.2005.9.129
6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in trypanosomatidae - Molecular characterization, database searches, modelling studies and evolutionary analysis
Chevalier, N., Bertrand, L., Rider, M. H., Opperdoes, F. R., Rigden, D. J., & Michels, P. A. M. (2005). 6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in trypanosomatidae - Molecular characterization, database searches, modelling studies and evolutionary analysis. FEBS JOURNAL, 272(14), 3542-3560. doi:10.1111/j.1742-4658.2005.04774.x
An inactivated nuclease-like domain in RecC with novel function: implications for evolution
Rigden, D. J. (2005). An inactivated nuclease-like domain in RecC with novel function: implications for evolution. BMC STRUCTURAL BIOLOGY, 5. doi:10.1186/1472-6807-5-9
OMICS-related research in South America
Galperin, M. Y., & Rigden, D. J. (2005). OMICS-related research in South America. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 9(1), 1. doi:10.1089/omi.2005.9.1
Characterization and functional investigation of an <i>Arabidopsis</i> cDNA encoding a homologue to the d-PGMase superfamily
Bourgis, F., Botha, F. C., Mani, S., Hiten, F. N., Rigden, D. J., & Verbruggen, N. (2005). Characterization and functional investigation of an <i>Arabidopsis</i> cDNA encoding a homologue to the d-PGMase superfamily. JOURNAL OF EXPERIMENTAL BOTANY, 56(414), 1129-1142. doi:10.1093/jxb/eri105
Monomorphic subtelomeric DNA in the filamentous fungus, <i>Metarhizium anisopliae</i>,contains a RecQ helicase-like gene
Inglis, P. W., Rigden, D. J., Mello, L. V., Louis, E. J., & Valadares-Inglis, M. C. (2005). Monomorphic subtelomeric DNA in the filamentous fungus, <i>Metarhizium anisopliae</i>,contains a RecQ helicase-like gene. MOLECULAR GENETICS AND GENOMICS, 274(1), 79-90. doi:10.1007/s00438-005-1154-5
Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of <i>Anticarsia gemmatalis</i> nucleopolyhedrovirus
Dalmolin, C. C., da Silva, F. R., Mello, L. V., Rigden, D. J., & Castro, M. E. B. (2005). Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of <i>Anticarsia gemmatalis</i> nucleopolyhedrovirus. VIRUS RESEARCH, 110(1-2), 99-109. doi:10.1016/j.virusres.2005.01.010
2004
Archaea recruited D-Tyr-tRNA<SUP>Tyr</SUP> deacylase for editing in Thr-tRNA synthetase
Rigden, D. J. (2004). Archaea recruited D-Tyr-tRNA<SUP>Tyr</SUP> deacylase for editing in Thr-tRNA synthetase. RNA, 10(12), 1845-1851. doi:10.1261/rna.7115404
L-ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor - X-ray structure and molecular modeling of enzyme-inhibitor complexes
Botzki, A., Rigden, D. J., Braun, S., Nukui, M., Salmen, S., Hoechstetter, J., . . . Buschauer, A. (2004). L-ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor - X-ray structure and molecular modeling of enzyme-inhibitor complexes. JOURNAL OF BIOLOGICAL CHEMISTRY, 279(44), 45990-45997. doi:10.1074/jbc.M406146200
The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution
Rigden, D. J., & Galperin, M. Y. (2004). The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution. JOURNAL OF MOLECULAR BIOLOGY, 343(4), 971-984. doi:10.1016/j.jmb.2004.08.077
Characterization of the ligandin site of maize glutathione S-transferase I
Axarli, I. A., Rigden, D. J., & Labrou, N. E. (2004). Characterization of the ligandin site of maize glutathione S-transferase I. BIOCHEMICAL JOURNAL, 382, 885-893. doi:10.1042/BJ20040298
A new type of antimicrobial protein with multiple histidines from the hard tick, <i>Amblyomma hebraeum</i>
Lai, R., Takeuchi, H., Lomas, L. O., Jonczy, J., Rigden, D. J., Rees, H. H., & Turner, P. C. (2004). A new type of antimicrobial protein with multiple histidines from the hard tick, <i>Amblyomma hebraeum</i>. FASEB JOURNAL, 18(10), 1447-+. doi:10.1096/fj.03-1154fje
Weeds, worms, and more. Papain's long-lost cousin, phytochelatin synthase
Rea, P. A., Vatamaniuk, O. K., & Rigden, D. J. (2004). Weeds, worms, and more. Papain's long-lost cousin, phytochelatin synthase. PLANT PHYSIOLOGY, 136(1), 2463-2474. doi:10.1104/pp.104.048579
A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C
Rigden, D. J. (2004). A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C. FEBS LETTERS, 569(1-3), 229-234. doi:10.1016/j.febslet.2004.05.071
Molecular cloning of a cysteine proteinase cDNA from the cotton boll weevil <i>Anthonomus grandis</i> (Coleoptera: Curculionidae)
Neto, O. B. D., Batista, J. A. N., Rigden, D. J., Franco, O. L., Fragoso, R. R., Monteiro, A. C. S., . . . Grossi-De-Sá, M. F. (2004). Molecular cloning of a cysteine proteinase cDNA from the cotton boll weevil <i>Anthonomus grandis</i> (Coleoptera: Curculionidae). BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 68(6), 1235-1242. doi:10.1271/bbb.68.1235
Engineering the pH-dependence of kinetic parameters of maize glutathione <i>S</i>-transferase I by site-directed mutagenesis
Labrou, N. E., Rigden, D. J., & Clonis, Y. D. (2004). Engineering the pH-dependence of kinetic parameters of maize glutathione <i>S</i>-transferase I by site-directed mutagenesis. BIOMOLECULAR ENGINEERING, 21(2), 61-66. doi:10.1016/j.bioeng.2003.10.002
Designed chimaeric galactosyl-mimodye ligands for the purification of <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase
Mazitsos, C. F., Rigden, D. J., & Clonis, Y. D. (2004). Designed chimaeric galactosyl-mimodye ligands for the purification of <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase. JOURNAL OF CHROMATOGRAPHY A, 1029(1-2), 103-112. doi:10.1016/j.chroma.2003.09.048
The structure-function relationship in the clostripain family of peptidases
Labrou, N. E., & Rigden, D. J. (2004). The structure-function relationship in the clostripain family of peptidases. EUROPEAN JOURNAL OF BIOCHEMISTRY, 271(5), 983-992. doi:10.1111/j.1432-1033.2004.04000.x
A diverse family of serine protemase genes expressed in cotton boll weevil (<i>Anthonomus grandis</i>):: implications for the design of pest-resistant transgenic cotton plants
Oliveira-Neto, O. B., Batista, J. A. N., Rigden, D. J., Fragoso, R. R., Silva, R. O., Gomes, E. A., . . . Grossi-de-Sá, M. F. (2004). A diverse family of serine protemase genes expressed in cotton boll weevil (<i>Anthonomus grandis</i>):: implications for the design of pest-resistant transgenic cotton plants. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY, 34(9), 903-918. doi:10.1016/j.ibmb.2004.06.001
A new type of antimicrobial protein with multiple histidines from the hard tick, Amblyomma hebraeum
Lai, R., Takeuchi, H., Lomas, L. O., Jonczy, J., Rigden, D. J., Rees, H. H., & Turner, P. C. (2004). A new type of antimicrobial protein with multiple histidines from the hard tick, Amblyomma hebraeum. Faseb Journal, 18(10), 162-178.
Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding specificity to alpha-amylases
da Silva, M. C. M., Mello, L. V., Coutinho, M. V., Rigden, D. J., Neshich, G., Chrispeels, M. J., & Grossi-De-Sá, M. F. (2004). Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding specificity to alpha-amylases. PESQUISA AGROPECUARIA BRASILEIRA, 39(3), 201-208. doi:10.1590/S0100-204X2004000300001
Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of <i>Streptococcus pneumoniae</i>
Bumbaca, D., Littlejohn, J. E., Nayakanti, H., Rigden, D. J., Galperin, M. Y., & Jedrzejas, M. J. (2004). Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of <i>Streptococcus pneumoniae</i>. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 8(4), 341-356. doi:10.1089/omi.2004.8.341
The PA14 domain, a conserved all-β domain in bacterial toxins, enzymes, adhesins and signaling molecules
Rigden, D. J., Mello, L. V., & Galperin, M. Y. (2004). The PA14 domain, a conserved all-β domain in bacterial toxins, enzymes, adhesins and signaling molecules. TRENDS IN BIOCHEMICAL SCIENCES, 29(7), 335-339. doi:10.1016/j.tibs.2004.05.002
2003
Structures of <i>Streptococcus pneumoniae</i> hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides -: Insights into specificity and mechanism of action
Rigden, D. J., & Jedrzejas, M. J. (2003). Structures of <i>Streptococcus pneumoniae</i> hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides -: Insights into specificity and mechanism of action. JOURNAL OF BIOLOGICAL CHEMISTRY, 278(50), 50596-50606. doi:10.1074/jbc.M307596200
Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of <i>Brachiaria brizantha</i>
Rodrigues, J. C. M., Cabral, G. B., Dusi, D. M. A., de Mello, L. V., Rigden, D. J., & Carneiro, V. T. C. (2003). Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of <i>Brachiaria brizantha</i>. PLANT MOLECULAR BIOLOGY, 53(6), 745-757. doi:10.1023/B:PLAN.0000023664.21910.bd
Fold recognition analysis of glycosyltransferase families: further members of structural superfamilies
Franco, O. L., & Rigden, D. J. (2003). Fold recognition analysis of glycosyltransferase families: further members of structural superfamilies. GLYCOBIOLOGY, 13(10), 707-712. doi:10.1093/glycob/cwg098
Use of phage display to select novel cystatins specific for <i>Acanthoscelides obtectus</i> cysteine proteinases
Melo, F. R., Mello, M. O., Franco, O. L., Rigden, D. J., Mello, L. V., Genú, A. M., . . . Grossi-de-Sá, M. F. (2003). Use of phage display to select novel cystatins specific for <i>Acanthoscelides obtectus</i> cysteine proteinases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1651(1-2), 146-152. doi:10.1016/S1570-9639(03)00264-4
The crystal structure of <i>Trypanosoma brucei</i> enolase:: Visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition
Giotto, M. T. D., Hannaert, V., Vertommen, D., Navarro, M. V. D. S., Rider, M. H., Michels, P. A. M., . . . Rigden, D. J. (2003). The crystal structure of <i>Trypanosoma brucei</i> enolase:: Visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition. JOURNAL OF MOLECULAR BIOLOGY, 331(3), 653-665. doi:10.1016/S0022-2836(03)00752-6
Genome-based identification of a carbohydrate binding module in <i>Streptococcus pneumoniae</i> hyaluronate lyase
Rigden, D. J., & Jedrzejas, M. J. (2003). Genome-based identification of a carbohydrate binding module in <i>Streptococcus pneumoniae</i> hyaluronate lyase. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 52(2), 203-211. doi:10.1002/prot.10405
Kinetic characterization, structure modelling studies and crystallization of <i>Trypanosoma brucei</i> enolase
Hannaert, V., Albert, M. A., Rigden, D. J., Giotto, M. T. D., Thiemann, O., Garratt, R. C., . . . Michels, P. A. M. (2003). Kinetic characterization, structure modelling studies and crystallization of <i>Trypanosoma brucei</i> enolase. EUROPEAN JOURNAL OF BIOCHEMISTRY, 270(15), 3205-3213. doi:10.1046/j.1432-1033.2003.03692.x
Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families
Rigden, D. J., Jedrzejas, M. J., & de Mello, L. V. (2003). Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families. FEBS LETTERS, 544(1-3), 103-111. doi:10.1016/s0014-5793(03)00481-2
Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling
Rigden, D. J., Lamani, E., Mello, L. V., Littlejohn, J. E., & Jedrzejas, M. J. (2003). Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. JOURNAL OF MOLECULAR BIOLOGY, 328(4), 909-920. doi:10.1016/S0022-2836(03)00350-4
Amidase domains from bacterial and phage autolysins define a family of γ-D,L-glutamate-specific amidohydrolases
Rigden, D. J., Jedrzejas, M. J., & Galperin, M. Y. (2003). Amidase domains from bacterial and phage autolysins define a family of γ-D,L-glutamate-specific amidohydrolases. TRENDS IN BIOCHEMICAL SCIENCES, 28(5), 230-234. doi:10.1016/S0968-0004(03)00062-8
An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands
Rigden, D. J., Jedrzejas, M. J., & Galperin, M. Y. (2003). An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands. FEMS MICROBIOLOGY LETTERS, 221(1), 103-110. doi:10.1016/S0378-1097(03)00160-5
Unexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase
Rigden, D. J. (2003). Unexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase. FEBS LETTERS, 536(1-3), 77-84. doi:10.1016/S0014-5793(03)00014-0
Plant-like traits associated with metabolism of <i>Trypanosoma</i> parasites
Hannaert, V., Saavedra, E., Duffieux, F., Szikora, J. P., Rigden, D. J., Michels, P. A. M., & Opperdoes, F. R. (2003). Plant-like traits associated with metabolism of <i>Trypanosoma</i> parasites. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(3), 1067-1071. doi:10.1073/pnas.0335769100
The structure of the D49 phospholipase A<sub>2</sub> piratoxin III from <i>Bothrops pirajai</i> reveals unprecedented structural displacement of the calcium-binding loop:: possible relationship to cooperative substrate binding
Rigden, D. J., Hwa, L. W., Marangoni, S., Toyama, M. H., & Polikarpov, I. (2003). The structure of the D49 phospholipase A<sub>2</sub> piratoxin III from <i>Bothrops pirajai</i> reveals unprecedented structural displacement of the calcium-binding loop:: possible relationship to cooperative substrate binding. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 59, 255-262. doi:10.1107/S0907444902021467
Structures of phosphate and trivanadate complexes of <i>Bacillus stearothermophilus</i> phosphatase PhoE:: Structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily
Rigden, D. J., Littlejohn, J. E., Henderson, K., & Jedrzejas, M. J. (2003). Structures of phosphate and trivanadate complexes of <i>Bacillus stearothermophilus</i> phosphatase PhoE:: Structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily. JOURNAL OF MOLECULAR BIOLOGY, 325(3), 411-420. doi:10.1016/S0022-2836(02)01229-9
Analysis of structure and function of putative surface-exposed proteins encoded in the <i>Streptococcus pneumoniae</i> genome:: A bioinformatics-based approach to vaccine and drug design
Rigden, D. J., Galperin, M. Y., & Jedrzejas, M. J. (2003). Analysis of structure and function of putative surface-exposed proteins encoded in the <i>Streptococcus pneumoniae</i> genome:: A bioinformatics-based approach to vaccine and drug design. CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 38(2), 143-168. doi:10.1080/713609215
Molecular cloning of α-amylases from cotton boll weevil, <i>Anthonomus grandis</i> and structural relations to plant inhibitors:: An approach to insect resistance
Oliveira-Neto, O. B., Batista, J. A. N., Rigden, D. J., Franco, O. L., Falcao, R., Fragoso, R. R., . . . Grossi-de-Sá, M. F. (2003). Molecular cloning of α-amylases from cotton boll weevil, <i>Anthonomus grandis</i> and structural relations to plant inhibitors:: An approach to insect resistance. JOURNAL OF PROTEIN CHEMISTRY, 22(1), 77-87. doi:10.1023/A:1023024012657
Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?
Rigden, D. J., Jedrzejas, M. J., Moroz, O. V., & Galperin, M. Y. (2003). Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?. TRENDS IN MICROBIOLOGY, 11(7), 295-297. doi:10.1016/S0966-842X(03)00153-7
2002
Galactosyl-mimodye ligands for <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase -: Design, synthesis and evaluation
Mazitsos, C. F., Rigden, D. J., Tsoungas, P. G., & Clonis, Y. D. (2002). Galactosyl-mimodye ligands for <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase -: Design, synthesis and evaluation. EUROPEAN JOURNAL OF BIOCHEMISTRY, 269(22), 5391-5405. doi:10.1046/j.1432-1033.2002.03211.x
Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from <i>Prosopis juliflora</i>
Franco, O. L., de Sá, M. F. G., Sales, M. P., Mello, L. V., Oliveira, A. S., & Rigden, D. J. (2002). Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from <i>Prosopis juliflora</i>. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 49(3), 335-341. doi:10.1002/prot.10228
Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture, modelling and assignment of catalytic residues.
Rigden, D. J., & Franco, O. L. (2002). Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture, modelling and assignment of catalytic residues.. FEBS letters, 530(1-3), 225-232. doi:10.1016/s0014-5793(02)03490-7
β-Helical catalytic domains in glycoside hydrolase families 49, 55 and 87:: domain architecture, modelling and assignment of catalytic residues
Rigden, D. J., & Franco, O. L. (2002). β-Helical catalytic domains in glycoside hydrolase families 49, 55 and 87:: domain architecture, modelling and assignment of catalytic residues. FEBS LETTERS, 530(1-3), 225-232. doi:10.1016/S0014-5793(02)03490-7
PrfA protein of <i>Bacillus</i> species:: Prediction and demonstration of endonuclease activity on DNA
Rigden, D. J., Setlow, P., Setlow, B., Bagyan, I., Stein, R. A., & Jedrzejas, M. J. (2002). PrfA protein of <i>Bacillus</i> species:: Prediction and demonstration of endonuclease activity on DNA. PROTEIN SCIENCE, 11(10), 2370-2381. doi:10.1110/ps.0216802
<i>Leishmania donovani</i> phosphofructokinase -: Gene characterization, biochemical properties and structure-modelling studies
López, C., Chevalier, N., Hannaert, V., Rigden, D. J., Michels, P. A. M., & Ramirez, J. L. (2002). <i>Leishmania donovani</i> phosphofructokinase -: Gene characterization, biochemical properties and structure-modelling studies. EUROPEAN JOURNAL OF BIOCHEMISTRY, 269(16), 3978-3989. doi:10.1046/j.1432-1033.2002.03086.x
Inhibition of trypsin by cowpea thionin:: Characterization, molecular modeling, and docking
Melo, F. R., Rigden, D. J., Franco, O. L., Mello, L. V., Ary, M. B., de Sá, M. F. G., & Bloch, C. (2002). Inhibition of trypsin by cowpea thionin:: Characterization, molecular modeling, and docking. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 48(2), 311-319. doi:10.1002/prot.10142
Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13
Rigden, D. J. (2002). Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13. FEBS LETTERS, 523(1-3), 17-22. doi:10.1016/S0014-5793(02)02879-X
Galactosyl-biomimetic dye-ligands for the purification of <i>Dactylium dendroides</i> galactose oxidase
Mazitsos, C. F., Rigden, D. J., Tsoungas, P. G., & Clonis, Y. D. (2002). Galactosyl-biomimetic dye-ligands for the purification of <i>Dactylium dendroides</i> galactose oxidase. JOURNAL OF CHROMATOGRAPHY A, 954(1-2), 137-150. doi:10.1016/S0021-9673(02)00176-0
The putative effector-binding site of <i>Leishmania mexicana</i> pyruvate kinase studied by site-directed mutagenesis
Hannaert, V., Yernaux, C., Rigden, D. J., Fothergill-Gilmore, L. A., Opperdoes, F. R., & Michels, P. A. M. (2002). The putative effector-binding site of <i>Leishmania mexicana</i> pyruvate kinase studied by site-directed mutagenesis. FEBS LETTERS, 514(2-3), 255-259. doi:10.1016/S0014-5793(02)02374-8
Plant α-amylase inhibitors and their interaction with insect α-amylases -: Structure, function and potential for crop protection
Franco, O. L., Rigden, D. J., Melo, F. R., & Grossi-de-Sá, M. F. (2002). Plant α-amylase inhibitors and their interaction with insect α-amylases -: Structure, function and potential for crop protection. EUROPEAN JOURNAL OF BIOCHEMISTRY, 269(2), 397-412. doi:10.1046/j.0014-2956.2001.02656.x
Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> with broad specificity phosphatase activity
Rigden, D. J., Mello, L. V., Setlow, P., & Jedrzejas, M. J. (2002). Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> with broad specificity phosphatase activity. JOURNAL OF MOLECULAR BIOLOGY, 315(5), 1129-1143. doi:10.1006/jmbi.2001.5290
Breaking the mould
Rigden, D. (2002). Breaking the mould. Petroleum Economist, 69(4), 4-6.
Deep gas potential emerges in shallow water
Rigden, D. (2002). Deep gas potential emerges in shallow water. Petroleum Economist, 69(6), 7-8.
Deeper and deeper
Rigden, D. (2002). Deeper and deeper. Petroleum Economist, 69(4), 7-8.
FPSOs: Market or mirage?
Rigden, D. (2002). FPSOs: Market or mirage?. Petroleum Economist, 69(6), 10-11.
Forging ahead
Rigden, D. (2002). Forging ahead. Petroleum Economist, 69(6), 34.
Plant α‐amylase inhibitors and their interaction with insect α‐amylases
Franco, O. L., Rigden, D. J., Melo, F. R., & Grossi‐de‐Sá, M. F. (2002). Plant α‐amylase inhibitors and their interaction with insect α‐amylases. European Journal of Biochemistry, 269(2), 397-412. doi:10.1046/j.0014-2956.2001.02656.x
Putative pathogenesis-related genes within <i>Solanum nigrum</i> L. var. <i>americanum</i> genome:: isolation of two genes coding for PR5-like proteins, phylogenetic and sequence analysis
Campos, M. A., Ribeiro, S. G., Rigden, D. J., Monte, D. C., & De Sa, M. F. G. (2002). Putative pathogenesis-related genes within <i>Solanum nigrum</i> L. var. <i>americanum</i> genome:: isolation of two genes coding for PR5-like proteins, phylogenetic and sequence analysis. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY, 61(4), 205-216. doi:10.1006/pmpp.2002.0430
Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors
Rigden, D. J., Mosolov, V. V., & Galperin, M. Y. (2002). Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors. PROTEIN SCIENCE, 11(8), 1971-1977. doi:10.1110/ps.0207202
Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments
Rigden, D. J. (2002). Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. PROTEIN ENGINEERING, 15(2), 65-77. doi:10.1093/protein/15.2.65
2001
Corrigendum to: The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin‐type fold and may have arisen by horizontal gene transfer (FEBS 25160)
Rigden, D. J., Monteiro, A. C. S., & Grossi de Sá, M. F. (2001). Corrigendum to: The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin‐type fold and may have arisen by horizontal gene transfer (FEBS 25160). FEBS Letters, 506(3), 296. doi:10.1016/s0014-5793(01)02933-7
The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer (FEBS 25160) (vol 504, pg 41, 2001)
Rigden, D. J., Monteiro, A. C. S., & de Sá, M. F. G. (2001). The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer (FEBS 25160) (vol 504, pg 41, 2001). FEBS LETTERS, 506(3), 296. doi:10.1016/S0014-5793(01)02933-7
A cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase
Rigden, D. J., Bagyan, I., Lamani, E., Setlow, P., & Jedrzejas, M. J. (2001). A cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase. PROTEIN SCIENCE, 10(9), 1835-1846. doi:10.1110/ps.15701
A cofactor‐dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase
Rigden, D. J., Bagyan, I., Lamani, E., Setlow, P., & Jedrzejas, M. J. (2001). A cofactor‐dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase. Protein Science, 10(9), 1835-1846. doi:10.1110/ps.15701
The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer
Rigden, D. J., Monteiro, A. C. S., & de Sá, M. F. G. (2001). The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer. FEBS LETTERS, 504(1-2), 41-44. doi:10.1016/S0014-5793(01)02753-3
New family of glutathionyl-biomimetic ligands for affinity chromatography of glutathione-recognising enzymes
Melissis, S. C., Rigden, D. J., & Clonis, Y. D. (2001). New family of glutathionyl-biomimetic ligands for affinity chromatography of glutathione-recognising enzymes. JOURNAL OF CHROMATOGRAPHY A, 917(1-2), 29-42. doi:10.1016/S0021-9673(01)00655-0
A novel heterodimeric antimicrobial peptide from the tree-frog <i>Phyllomedusa distincta</i>
Batista, C. V. F., Scaloni, A., Rigden, D. J., Silva, L. R., Romero, A. R., Dukor, R., . . . Bloch, C. (2001). A novel heterodimeric antimicrobial peptide from the tree-frog <i>Phyllomedusa distincta</i>. FEBS LETTERS, 494(1-2), 85-89. doi:10.1016/S0014-5793(01)02324-9
Active-site characterization of <i>Candida boidinii</i> formate dehydrogenase
Labrou, N. E., & Rigden, D. J. (2001). Active-site characterization of <i>Candida boidinii</i> formate dehydrogenase. BIOCHEMICAL JOURNAL, 354, 455-463. doi:10.1042/0264-6021:3540455
Active-site characterization of Candida boidinii formate dehydrogenase
LABROU, N. E., & RIGDEN, D. J. (2001). Active-site characterization of Candida boidinii formate dehydrogenase. Biochemical Journal, 354(2), 455-463. doi:10.1042/bj3540455
2000
Characterization of active-site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase -: Elucidation of the roles of amino acids involved in substrate binding and catalysis
Nairn, J., Duncan, D., Price, N. E., Kelly, S. M., Fothergill-Gilmore, L. A., Uhrinova, S., . . . Price, N. C. (2000). Characterization of active-site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase -: Elucidation of the roles of amino acids involved in substrate binding and catalysis. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(24), 7065-7074. doi:10.1046/j.1432-1327.2000.01802.x
Characterization of active‐site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase
Nairn, J., Duncan, D., Price, N. E., Kelly, S. M., Fothergill‐Gilmore, L. A., Uhrinova, S., . . . Price, N. C. (2000). Characterization of active‐site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase. European Journal of Biochemistry, 267(24), 7065-7074. doi:10.1046/j.1432-1327.2000.01802.x
Purification, biochemical characterisation and partial primary structure of a new α-amylase inhibitor from <i>Secale cereale</i> (rye)
Iulek, J., Franco, O. L., Silva, M., Slivinski, C. T., Bloch, C., Rigden, D. J., & de Sá, M. F. G. (2000). Purification, biochemical characterisation and partial primary structure of a new α-amylase inhibitor from <i>Secale cereale</i> (rye). INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 32(11-12), 1195-1204. doi:10.1016/S1357-2725(00)00053-4
Characterization of the NAD<SUP>+</SUP> binding site of <i>Candida boidinii</i> formate dehydrogenase by affinity labelling and site-directed mutagenesis
Labrou, N. E., Rigden, D. J., & Clonis, Y. D. (2000). Characterization of the NAD<SUP>+</SUP> binding site of <i>Candida boidinii</i> formate dehydrogenase by affinity labelling and site-directed mutagenesis. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(22), 6657-6664. doi:10.1046/j.1432-1327.2000.01761.x
Structural modeling of a plant disease resistance gene product domain
Rigden, D. J., Mello, L. V., & Bertioli, D. J. (2000). Structural modeling of a plant disease resistance gene product domain. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 41(1), 133-143. doi:3.0.CO;2-M">10.1002/1097-0134(20001001)41:1<133::AID-PROT150>3.0.CO;2-M
Activity of wheat α-amylase inhibitors towards bruchid α-amylases and structural explanation of observed specificities
Franco, O. L., Rigden, D. J., Melo, F. R., Bloch, C., Silva, C. P., & de Sá, M. F. G. (2000). Activity of wheat α-amylase inhibitors towards bruchid α-amylases and structural explanation of observed specificities. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(8), 2166-2173. doi:10.1046/j.1432-1327.2000.01199.x
Glycerol kinase of <i>Trypanosoma brucei</i> -: Cloning, molecular characterization and mutagenesis
Králová, I., Rigden, D. J., Opperdoes, F. R., & Michels, P. A. M. (2000). Glycerol kinase of <i>Trypanosoma brucei</i> -: Cloning, molecular characterization and mutagenesis. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(8), 2323-2333. doi:10.1046/j.1432-1327.2000.01238.x
Glycerol kinase of <i>Trypanosoma brucei</i>
Králová, I., Rigden, D. J., Opperdoes, F. R., & Michels, P. A. M. (2000). Glycerol kinase of <i>Trypanosoma brucei</i>. European Journal of Biochemistry, 267(8), 2323-2333. doi:10.1046/j.1432-1327.2000.01238.x
<i>Trypanosoma brucei</i> contains a 2,3-bisphosphoglycerate independent phosphoglycerate mutase
Chevalier, N., Rigden, D. J., Van Roy, J., Opperdoes, F. R., & Michels, P. A. M. (2000). <i>Trypanosoma brucei</i> contains a 2,3-bisphosphoglycerate independent phosphoglycerate mutase. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(5), 1464-1472. doi:10.1046/j.1432-1327.2000.01145.x
<i>Leishmania</i> pyruvate kinase:: the crystal structure reveals the structural basis of its unique regulatory properties
Fothergill-Gilmore, L. A., Rigden, D. J., Michels, P. A. M., & Phillips, S. E. V. (2000). <i>Leishmania</i> pyruvate kinase:: the crystal structure reveals the structural basis of its unique regulatory properties. BIOCHEMICAL SOCIETY TRANSACTIONS, 28, 186-190. doi:10.1042/bst0280186
Leishmania pyruvate kinase: the crystal structure reveals the structural basis of its unique regulatory properties
Fothergill-Gilmore, L. A., & Rigden, D. J. (2000). Leishmania pyruvate kinase: the crystal structure reveals the structural basis of its unique regulatory properties. Biochemical Society Transactions, 28(1), A12. doi:10.1042/bst028a012a
Design and synthesis of germline-based hemi-humanized single-chain Fv against the CD18 surface antigen
Caldas, C., Coelho, V. P. C. V., Rigden, D. J., Neschich, G., Moro, A. M., & Brígido, M. M. (2000). Design and synthesis of germline-based hemi-humanized single-chain Fv against the CD18 surface antigen. PROTEIN ENGINEERING, 13(5), 353-360. doi:10.1093/protein/13.5.353
Structural modeling of a plant disease resistance gene product domain
Rigden, D. J., Mello, L. V., & Bertioli, D. J. (2000). Structural modeling of a plant disease resistance gene product domain. Proteins, 41(1), 133-143.
1999
A structural model for the <i>rol</i>A protein and its interaction with DNA
Rigden, D. J., & Carneiro, M. (1999). A structural model for the <i>rol</i>A protein and its interaction with DNA. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 37(4), 697-708. doi:3.0.CO;2-Y">10.1002/(SICI)1097-0134(19991201)37:4<697::AID-PROT18>3.0.CO;2-Y
Manifesting heterozygotes in a Japanese family with a novel mutation in the muscle-specific phosphoglycerate mutase (PGAM-M) gene
Hadjigeorgiou, G. M., Kawashima, N., Bruno, C., Andreu, A. L., Sue, C. M., Rigden, D. J., . . . DiMauro, S. (1999). Manifesting heterozygotes in a Japanese family with a novel mutation in the muscle-specific phosphoglycerate mutase (PGAM-M) gene. NEUROMUSCULAR DISORDERS, 9(6-7), 399-402. doi:10.1016/S0960-8966(99)00039-5
The structure of pyruvate kinase from <i>Leishmania mexicana</i> reveals details of the allosteric transition and unusual effector specificity
Rigden, D. J., Phillips, S. E. V., Michels, P. A. M., & Fothergill-Gilmore, L. A. (1999). The structure of pyruvate kinase from <i>Leishmania mexicana</i> reveals details of the allosteric transition and unusual effector specificity. JOURNAL OF MOLECULAR BIOLOGY, 291(3), 615-635. doi:10.1006/jmbi.1999.2918
Structure-activity studies on cysteine-substituted neurokinin A analogs
Labrou, N. E., Mello, L. V., Rigden, D. J., Keen, J. N., & Findlay, J. B. C. (1999). Structure-activity studies on cysteine-substituted neurokinin A analogs. PEPTIDES, 20(7), 795-801. doi:10.1016/S0196-9781(99)00064-9
Polyanionic inhibitors of phosphoglycerate mutase: Combined structural and biochemical analysis
Rigden, D. J., Walter, R. A., Phillips, S. E. V., & Fothergill-Gilmore, L. A. (1999). Polyanionic inhibitors of phosphoglycerate mutase: Combined structural and biochemical analysis. JOURNAL OF MOLECULAR BIOLOGY, 289(4), 691-699. doi:10.1006/jmbi.1999.2848
Sulphate ions observed in the 2.12 Å structure of a new crystal form of <i>S-cerevisiae</i> phosphoglycerate mutase provide insights into understanding the catalytic mechanism
Rigden, D. J., Walter, R. A., Phillips, S. E. V., & Fothergill-Gilmore, L. A. (1999). Sulphate ions observed in the 2.12 Å structure of a new crystal form of <i>S-cerevisiae</i> phosphoglycerate mutase provide insights into understanding the catalytic mechanism. JOURNAL OF MOLECULAR BIOLOGY, 286(5), 1507-1517. doi:10.1006/jmbi.1999.2566
Structure-activity studies on cysteine-substituted neurokinin A analogs
Labrou, N. E., Mello, L. V., Rigden, D. J., Keen, J. N., & Findlay, J. B. (1999). Structure-activity studies on cysteine-substituted neurokinin A analogs. Peptides, 20(7), 795-801.
The role of the C-terminal region in phosphoglycerate mutase
Walter, R. A., Nairn, J., Duncan, D., Price, N. C., Kelly, S. M., Rigden, D. J., & Fothergill-Gilmore, L. A. (1999). The role of the C-terminal region in phosphoglycerate mutase. BIOCHEMICAL JOURNAL, 337, 89-95. doi:10.1042/0264-6021:3370089
The role of the C-terminal region in phosphoglycerate mutase
WALTER, R. A., NAIRN, J., DUNCAN, D., PRICE, N. C., KELLY, S. M., RIGDEN, D. J., & FOTHERGILL-GILMORE, L. A. (1999). The role of the C-terminal region in phosphoglycerate mutase. Biochemical Journal, 337(1), 89-95. doi:10.1042/bj3370089
The structure of pyruvate kinase from <i>Leishmania mexicana</i> reveals details of the allosteric transition and unusual effector specificity (vol 291, pg 615, 1999)
Rigden, D. J., Phillips, S. E. V., Michels, P. A. M., & Fothergill-Gilmore, L. A. (1999). The structure of pyruvate kinase from <i>Leishmania mexicana</i> reveals details of the allosteric transition and unusual effector specificity (vol 291, pg 615, 1999). JOURNAL OF MOLECULAR BIOLOGY, 293(3), 745-749. doi:10.1006/jmbi.1999.3170
1998
The 2.3 Å X-ray crystal structure of <i>S-cerevisiae</i> phosphoglycerate mutase
Rigden, D. J., Alexeev, D., Phillips, S. E. V., & Fothergill-Gilmore, L. A. (1998). The 2.3 Å X-ray crystal structure of <i>S-cerevisiae</i> phosphoglycerate mutase. JOURNAL OF MOLECULAR BIOLOGY, 276(2), 449-459. doi:10.1006/jmbi.1997.1554
1997
The glycosomal ATP-dependent phosphofructokinase of <i>Trypanosoma brucei</i> must have evolved from an ancestral pyrophosphate-dependent enzyme
Michels, P. A. M., Chevalier, N., Opperdoes, F. R., Rider, M. H., & Rigden, D. J. (1997). The glycosomal ATP-dependent phosphofructokinase of <i>Trypanosoma brucei</i> must have evolved from an ancestral pyrophosphate-dependent enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY, 250(3), 698-704. doi:10.1111/j.1432-1033.1997.00698.x
1996
Phosphoglycerate mutase from Schizosaccharomyces pombe: Development of an expression system and characterisation of three histidine mutants of the enzyme
Nairn, J., Price, N. C., Kelly, S. M., Rigden, D., FothergillGilmore, L. A., & Krell, T. (1996). Phosphoglycerate mutase from Schizosaccharomyces pombe: Development of an expression system and characterisation of three histidine mutants of the enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEIN STRUCTURE AND MOLECULAR ENZYMOLOGY, 1296(1), 69-75. doi:10.1016/0167-4838(96)00046-5
Cloning and sequencing of a gene encoding pyruvate kinase from Schizosaccharomyces pombe: implications for quaternary structure and regulation of the enzyme
NAIRN, J., SMITH, S., ALLISON, P., RIGDEN, D., FOTHERGILLGILMORE, L., & PRICE, N. (1996). Cloning and sequencing of a gene encoding pyruvate kinase from Schizosaccharomyces pombe: implications for quaternary structure and regulation of the enzyme. FEMS Microbiology Letters, 136(3), 329. doi:10.1016/0378-1097(96)00035-3
Erratum to âCloning and sequencing of a gene encoding pyruvate kinase from<i>Schizosaccharomyces pombe</i>: implications for quaternary structure and regulation of the enzymeâ [FEMS Microbiol. Lett. 134 (1995) 221â226]
Nairn, J., Smith, S., Allison, P. J., Rigden, D., Fothergill-Gilmore, L. A., & Price, N. C. (1996). Erratum to âCloning and sequencing of a gene encoding pyruvate kinase from<i>Schizosaccharomyces pombe</i>: implications for quaternary structure and regulation of the enzymeâ [FEMS Microbiol. Lett. 134 (1995) 221â226]. FEMS Microbiology Letters, 136(3), 329. doi:10.1111/j.1574-6968.1996.tb08069.x
1995
CLONING AND SEQUENCING OF A GENE ENCODING PYRUVATE-KINASE FROM SCHIZOSACCHAROMYCES-POMBE - IMPLICATIONS FOR QUATERNARY STRUCTURE AND REGULATION OF THE ENZYME
NAIRN, J., SMITH, S., ALLISON, P. J., RIGDEN, D., FOTHERGILLGILMORE, L. A., & PRICE, N. C. (1995). CLONING AND SEQUENCING OF A GENE ENCODING PYRUVATE-KINASE FROM SCHIZOSACCHAROMYCES-POMBE - IMPLICATIONS FOR QUATERNARY STRUCTURE AND REGULATION OF THE ENZYME. FEMS MICROBIOLOGY LETTERS, 134(2-3), 221-226. doi:10.1111/j.1574-6968.1995.tb07941.x
Cloning and sequencing of a gene encoding pyruvate kinase from Schizosaccharomyces pombe; implications for quaternary structure and regulation of the enzyme
Nairn, J. (1995). Cloning and sequencing of a gene encoding pyruvate kinase from Schizosaccharomyces pombe; implications for quaternary structure and regulation of the enzyme. FEMS Microbiology Letters, 134(2-3), 221-226. doi:10.1016/0378-1097(95)00408-3
1990
Human adipose tissue glycogen levels and responses to carbohydrate feeding
Rigden, D. J., Jellyman, A. E., Frayn, K. N., & Coppack, S. W. (1990). Human adipose tissue glycogen levels and responses to carbohydrate feeding. Eur J Clin Nutr, 44(9), 689-692.