Publications
2024
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
Deep-learning protein structure predictions suggest likely molecular functions for three uncharacterised polytopic membrane proteins from the<i>P. falciparum</i>apicoplast
2023
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
Cover Image, Volume 91, Issue 12
Das, R., Kretsch, R. C., Simpkin, A. J., Mulvaney, T., Pham, P., Rangan, R., . . . Westhof, E. (2023). Cover Image, Volume 91, Issue 12. Proteins: Structure, Function, and Bioinformatics, 91(12). doi:10.1002/prot.26640
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
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
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
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
Tertiary structure assessment at CASP15
2022
Structural Insights into Pink-eyed Dilution Protein (Oca2)
<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
<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
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
<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
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
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
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
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/
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
Evaluation of model refinement in CASP14
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
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.
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
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
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.
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
CCP4 CLOUD FOR DISTRIBUTED CRYSTALLOGRAPHIC COMPUTATIONS
Krissinel, E., Lebedev, A., Uski, V., Ballard, C., Keegan, R., Nicholls, R., . . . Skubak, P. (2019). CCP4 CLOUD FOR DISTRIBUTED CRYSTALLOGRAPHIC COMPUTATIONS. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 75 (pp. E171). doi:10.1107/S2053273319093859
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
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
2018
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
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
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
2017
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/
2016
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
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