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For: Read RJ, Sammito MD, Kryshtafovych A, Croll TI. Evaluation of model refinement in CASP13. Proteins 2019;87:1249-1262. [PMID: 31365160 PMCID: PMC6851427 DOI: 10.1002/prot.25794] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/03/2019] [Accepted: 07/27/2019] [Indexed: 12/25/2022]
Number Cited by Other Article(s)
1
In silico design of a polypeptide as a vaccine candidate against ascariasis. Sci Rep 2023;13:3504. [PMID: 36864139 PMCID: PMC9981566 DOI: 10.1038/s41598-023-30445-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023]  Open
2
Holland J, Grigoryan G. Structure‐conditioned amino‐acid couplings: how contact geometry affects pairwise sequence preferences. Protein Sci 2022;31:900-917. [PMID: 35060221 PMCID: PMC8927866 DOI: 10.1002/pro.4280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/11/2022]
3
Verburgt J, Kihara D. Benchmarking of structure refinement methods for protein complex models. Proteins 2022;90:83-95. [PMID: 34309909 PMCID: PMC8671191 DOI: 10.1002/prot.26188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 01/03/2023]
4
Simpkin AJ, Rodríguez FS, Mesdaghi S, Kryshtafovych A, Rigden DJ. Evaluation of model refinement in CASP14. Proteins 2021;89:1852-1869. [PMID: 34288138 PMCID: PMC8616799 DOI: 10.1002/prot.26185] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/19/2021] [Accepted: 07/11/2021] [Indexed: 12/15/2022]
5
Heo L, Janson G, Feig M. Physics-based protein structure refinement in the era of artificial intelligence. Proteins 2021;89:1870-1887. [PMID: 34156124 PMCID: PMC8616793 DOI: 10.1002/prot.26161] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 12/21/2022]
6
Kryshtafovych A, Moult J, Billings WM, Della Corte D, Fidelis K, Kwon S, Olechnovič K, Seok C, Venclovas Č, Won J. Modeling SARS-CoV-2 proteins in the CASP-commons experiment. Proteins 2021;89:1987-1996. [PMID: 34462960 PMCID: PMC8616790 DOI: 10.1002/prot.26231] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 01/21/2023]
7
Millán C, Keegan RM, Pereira J, Sammito MD, Simpkin AJ, McCoy AJ, Lupas AN, Hartmann MD, Rigden DJ, Read RJ. Assessing the utility of CASP14 models for molecular replacement. Proteins 2021;89:1752-1769. [PMID: 34387010 PMCID: PMC8881082 DOI: 10.1002/prot.26214] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022]
8
Adiyaman R, McGuffin LJ. ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts. Nucleic Acids Res 2021;49:W589-W596. [PMID: 34009387 PMCID: PMC8218204 DOI: 10.1093/nar/gkab300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]  Open
9
Shuvo MH, Gulfam M, Bhattacharya D. DeepRefiner: high-accuracy protein structure refinement by deep network calibration. Nucleic Acids Res 2021;49:W147-W152. [PMID: 33999209 PMCID: PMC8262753 DOI: 10.1093/nar/gkab361] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/18/2021] [Accepted: 04/23/2021] [Indexed: 12/20/2022]  Open
10
Jing X, Xu J. Fast and effective protein model refinement using deep graph neural networks. NATURE COMPUTATIONAL SCIENCE 2021;1:462-469. [PMID: 35321360 DOI: 10.1038/s43588-021-00098-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
11
Kapla J, Rodríguez-Espigares I, Ballante F, Selent J, Carlsson J. Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PLoS Comput Biol 2021;17:e1008936. [PMID: 33983933 PMCID: PMC8186765 DOI: 10.1371/journal.pcbi.1008936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/08/2021] [Accepted: 04/02/2021] [Indexed: 01/14/2023]  Open
12
Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy. Int J Mol Sci 2021;22:ijms22094408. [PMID: 33922489 PMCID: PMC8122964 DOI: 10.3390/ijms22094408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/02/2022]  Open
13
Hiranuma N, Park H, Baek M, Anishchenko I, Dauparas J, Baker D. Improved protein structure refinement guided by deep learning based accuracy estimation. Nat Commun 2021;12:1340. [PMID: 33637700 PMCID: PMC7910447 DOI: 10.1038/s41467-021-21511-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/18/2021] [Indexed: 11/22/2022]  Open
14
Heo L, Arbour CF, Janson G, Feig M. Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation. J Chem Theory Comput 2021;17:1931-1943. [PMID: 33562962 DOI: 10.1021/acs.jctc.0c01238] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
15
Brini E, Simmerling C, Dill K. Protein storytelling through physics. Science 2021;370:370/6520/eaaz3041. [PMID: 33243857 DOI: 10.1126/science.aaz3041] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
16
McCoy AJ, Stockwell DH, Sammito MD, Oeffner RD, Hatti KS, Croll TI, Read RJ. Phasertng: directed acyclic graphs for crystallographic phasing. Acta Crystallogr D Struct Biol 2021;77:1-10. [PMID: 33404520 PMCID: PMC7787104 DOI: 10.1107/s2059798320014746] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 11/06/2020] [Indexed: 12/01/2022]  Open
17
Jin S, Miller MD, Chen M, Schafer NP, Lin X, Chen X, Phillips GN, Wolynes PG. Molecular-replacement phasing using predicted protein structures from AWSEM-Suite. IUCRJ 2020;7:1168-1178. [PMID: 33209327 PMCID: PMC7642774 DOI: 10.1107/s2052252520013494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
18
Abriata LA, Dal Peraro M. Will Cryo-Electron Microscopy Shift the Current Paradigm in Protein Structure Prediction? J Chem Inf Model 2020;60:2443-2447. [PMID: 32134661 DOI: 10.1021/acs.jcim.0c00177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
19
Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci U S A 2020;117:1496-1503. [PMID: 31896580 DOI: 10.1073/pnas.1914677117] [Citation(s) in RCA: 806] [Impact Index Per Article: 201.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
20
Heo L, Feig M. High-accuracy protein structures by combining machine-learning with physics-based refinement. Proteins 2019;88:637-642. [PMID: 31693199 DOI: 10.1002/prot.25847] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/05/2019] [Accepted: 11/03/2019] [Indexed: 12/16/2022]
21
Kryshtafovych A, Schwede T, Topf M, Fidelis K, Moult J. Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins 2019;87:1011-1020. [PMID: 31589781 DOI: 10.1002/prot.25823] [Citation(s) in RCA: 281] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
22
Read RJ, Sammito MD, Kryshtafovych A, Croll TI. Evaluation of model refinement in CASP13. Proteins 2019;87:1249-1262. [PMID: 31365160 PMCID: PMC6851427 DOI: 10.1002/prot.25794] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/03/2019] [Accepted: 07/27/2019] [Indexed: 12/25/2022]
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