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For: Dhawanjewar AS, Roy AA, Madhusudhan MS. A knowledge-based scoring function to assess quaternary associations of proteins. Bioinformatics 2020;36:3739-3748. [PMID: 32246820 DOI: 10.1093/bioinformatics/btaa207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/01/2020] [Accepted: 03/30/2020] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Shirali A, Stebliankin V, Karki U, Shi J, Chapagain P, Narasimhan G. A comprehensive survey of scoring functions for protein docking models. BMC Bioinformatics 2025;26:25. [PMID: 39844036 PMCID: PMC11755896 DOI: 10.1186/s12859-024-05991-4] [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: 07/04/2024] [Accepted: 11/18/2024] [Indexed: 01/24/2025]  Open
2
Oriol F, Alberto M, Joachim AP, Patrick G, M BP, Ruben MF, Jaume B, Altair CH, Ferran P, Oriol G, Narcis FF, Baldo O. Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements. NAR Genom Bioinform 2024;6:lqae068. [PMID: 38867914 PMCID: PMC11167492 DOI: 10.1093/nargab/lqae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/18/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024]  Open
3
Sen N, Madhusudhan MS. A structural database of chain–chain and domain–domain interfaces of proteins. Protein Sci 2022. [DOI: 10.1002/pro.4406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
4
Sen N, Anishchenko I, Bordin N, Sillitoe I, Velankar S, Baker D, Orengo C. Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. Brief Bioinform 2022;23:bbac187. [PMID: 35641150 PMCID: PMC9294430 DOI: 10.1093/bib/bbac187] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 12/12/2022]  Open
5
Rajendran M, Ferran MC, Babbitt GA. Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics. BIOPHYSICAL REPORTS 2022;2:100056. [PMID: 35403093 PMCID: PMC8978532 DOI: 10.1016/j.bpr.2022.100056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/31/2022] [Indexed: 01/08/2023]
6
Guo L, He J, Lin P, Huang SY, Wang J. TRScore: a three-dimensional RepVGG-based scoring method for ranking protein docking models. Bioinformatics 2022;38:2444-2451. [PMID: 35199137 DOI: 10.1093/bioinformatics/btac120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022]  Open
7
Sharma VK, Lahiri M. Interplay between p300 and HDAC1 regulate acetylation and stability of Api5 to regulate cell proliferation. Sci Rep 2021;11:16427. [PMID: 34385547 PMCID: PMC8361156 DOI: 10.1038/s41598-021-95941-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022]  Open
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