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For: 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Garg P, Singhal G, Kulkarni P, Horne D, Salgia R, Singhal SS. Artificial Intelligence-Driven Computational Approaches in the Development of Anticancer Drugs. Cancers (Basel) 2024;16:3884. [PMID: 39594838 PMCID: PMC11593155 DOI: 10.3390/cancers16223884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 11/13/2024] [Accepted: 11/16/2024] [Indexed: 11/28/2024]  Open
2
Li G, Yuan Y, Zhang R. Predicting Protein-Ligand Binding Affinity Using Fusion Model of Spatial-Temporal Graph Neural Network and 3D Structure-Based Complex Graph. Interdiscip Sci 2024:10.1007/s12539-024-00644-9. [PMID: 39541085 DOI: 10.1007/s12539-024-00644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 11/16/2024]
3
Bayarsaikhan B, Zsidó BZ, Börzsei R, Hetényi C. Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols. Int J Mol Sci 2024;25:5945. [PMID: 38892133 PMCID: PMC11172440 DOI: 10.3390/ijms25115945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]  Open
4
Li J, Wang L, Zhu Z, Song C. Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction. J Chem Inf Model 2024;64:301-315. [PMID: 38117138 PMCID: PMC10777399 DOI: 10.1021/acs.jcim.3c01381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
5
Adiyaman R, Edmunds NS, Genc AG, Alharbi SMA, McGuffin LJ. Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process. BIOINFORMATICS ADVANCES 2023;3:vbad078. [PMID: 37359722 PMCID: PMC10290552 DOI: 10.1093/bioadv/vbad078] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023]
6
Alfonso-Prieto M, Capelli R. Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study. J Chem Inf Model 2023;63:2911-2917. [PMID: 37145455 DOI: 10.1021/acs.jcim.3c00380] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
7
Wu T, Guo Z, Cheng J. Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer. Bioinformatics 2023;39:btad298. [PMID: 37144951 PMCID: PMC10191610 DOI: 10.1093/bioinformatics/btad298] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 03/18/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]  Open
8
Avery C, Patterson J, Grear T, Frater T, Jacobs DJ. Protein Function Analysis through Machine Learning. Biomolecules 2022;12:1246. [PMID: 36139085 PMCID: PMC9496392 DOI: 10.3390/biom12091246] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022]  Open
9
Hong Y, Lee J, Ko J. A-Prot: protein structure modeling using MSA transformer. BMC Bioinformatics 2022;23:93. [PMID: 35296230 PMCID: PMC8925138 DOI: 10.1186/s12859-022-04628-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/03/2022] [Indexed: 11/18/2022]  Open
10
Hegedűs T, Geisler M, Lukács GL, Farkas B. Ins and outs of AlphaFold2 transmembrane protein structure predictions. Cell Mol Life Sci 2022;79:73. [PMID: 35034173 PMCID: PMC8761152 DOI: 10.1007/s00018-021-04112-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/25/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
11
Cao Y, Yang R, Wang W, Jiang S, Yang C, Liu N, Dai H, Lee I, Meng X, Yuan Z. Probing the Formation, Structure and Free Energy Relationships of M Protein Dimers of SARS-CoV-2. Comput Struct Biotechnol J 2022;20:573-582. [PMID: 35047128 PMCID: PMC8756865 DOI: 10.1016/j.csbj.2022.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022]  Open
12
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]
13
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]
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