2023
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.26602DOI: 10.1002/prot.26602
Cover Image, Volume 91, Issue 12 (Journal article)
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.26640DOI: 10.1002/prot.26640
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.26593DOI: 10.1002/prot.26593
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/S2059798323006289DOI: 10.1107/S2059798323006289
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/bsr20230060DOI: 10.1042/bsr20230060
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/S2059798323003595DOI: 10.1107/S2059798323003595
2022
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/S2059798322007987DOI: 10.1107/S2059798322007987
<i>Slice'N'Dice</i>: maximising predicted models for structural biologists (Journal article)
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/s2053273322096474DOI: 10.1107/s2053273322096474
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/S2059798322003576DOI: 10.1107/S2059798322003576
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-zDOI: 10.1038/s41564-021-01054-z
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/s2052252521011088DOI: 10.1107/s2052252521011088
2021
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.26214DOI: 10.1002/prot.26214
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.26185DOI: 10.1002/prot.26185
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.26171DOI: 10.1002/prot.26171
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/S2059798321009165DOI: 10.1107/S2059798321009165
Exploiting new generation ab initio and homology models from databases for MR (Conference Paper)
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/
ConPlot: web-based application for the visualization of protein contact maps integrated with other data (Journal article)
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/btab049DOI: 10.1093/bioinformatics/btab049
ConPlot: web-based application for the visualization of protein contact maps integrated with other data. (Journal article)
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
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/S205979832001133XDOI: 10.1107/S205979832001133X
Rodríguez, F. S., Simpkin, A., Davies, O., Keegan, R., & Rigden, D. (2020). Helical ensembles out-perform ideal helices in Molecular Replacement. doi:10.1101/2020.06.16.154690DOI: 10.1101/2020.06.16.154690
Simpkin, A. (2020, January 29). Exploring unconventional approaches to Molecular Replacement in X-ray crystallography with SIMBAD.
2019
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/S2059798319013962DOI: 10.1107/S2059798319013962
CCP4 CLOUD FOR DISTRIBUTED CRYSTALLOGRAPHIC COMPUTATIONS (Conference Paper)
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/S2053273319093859DOI: 10.1107/S2053273319093859
MOLECULAR REPLACEMENT USING STRUCTURE PREDICTIONS FROM NEW GENERATION DATABASES (Conference Paper)
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/S2053273319093732DOI: 10.1107/S2053273319093732
SIMBAD: STRUCTURE BASED SEARCH MODEL IDENTIFICATION FOR MOLECULAR REPLACEMENT USING THE PDB DATABASE (Conference Paper)
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/S2053273319093793DOI: 10.1107/S2053273319093793
2018
Identification of contaminants with SIMBAD: A Sequence-independent molecular replacement pipeline (Conference Paper)
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/S2053273318092641DOI: 10.1107/S2053273318092641
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/S2059798318005752DOI: 10.1107/S2059798318005752
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/S2059798318002310DOI: 10.1107/S2059798318002310
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/S2059798318003455DOI: 10.1107/S2059798318003455
2017
SIMBAD: A Sequence-independent molecular replacement pipeline (Conference Paper)
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/S2053273317085709DOI: 10.1107/S2053273317085709
SIMBAD: A Sequence-independent molecular replacement pipeline (Conference Paper)
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 (Conference Paper)
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/S2053273316096996DOI: 10.1107/S2053273316096996
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/s13104-016-2149-5DOI: 10.1186/s13104-016-2149-5
