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For: Brysbaert G, Lensink MF. Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein–Protein Binding. Front Bioinform 2021;1:684970. [PMID: 36303777 PMCID: PMC9581030 DOI: 10.3389/fbinf.2021.684970] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Gromiha MM, Pandey M, Kulandaisamy A, Sharma D, Ridha F. Progress on the development of prediction tools for detecting disease causing mutations in proteins. Comput Biol Med 2024;185:109510. [PMID: 39637461 DOI: 10.1016/j.compbiomed.2024.109510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 11/27/2024] [Accepted: 11/29/2024] [Indexed: 12/07/2024]
2
Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. J Chem Inf Model 2024;64:1331-1346. [PMID: 38346324 PMCID: PMC11144062 DOI: 10.1021/acs.jcim.3c01615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
3
Soto P, Gloeb GM, Tsuchida KA, Charles AA, Greenwood NM, Hendrickson H. Insight into the conserved structural dynamics of the C-terminus of mammal PrPC identifies structural core and possible structural role of pharmacological chaperones. Prion 2023;17:55-66. [PMID: 36892160 PMCID: PMC10012922 DOI: 10.1080/19336896.2023.2186674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]  Open
4
Rosignoli S, di Paola L, Paiardini A. PyPCN: protein contact networks in PyMOL. Bioinformatics 2023;39:btad675. [PMID: 37941462 PMCID: PMC10641099 DOI: 10.1093/bioinformatics/btad675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/25/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]  Open
5
Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550226. [PMID: 37547015 PMCID: PMC10402003 DOI: 10.1101/2023.07.23.550226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
6
Postel Z, Mauri T, Lensink MF, Touzet P. What is the potential impact of genetic divergence of plastid ribosomal genes between Silene nutans lineages in hybrids? An in silico approach using the 3D structure of the plastid ribosome. FRONTIERS IN PLANT SCIENCE 2023;14:1167478. [PMID: 37223795 PMCID: PMC10201985 DOI: 10.3389/fpls.2023.1167478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/25/2023]
7
Franke L, Peter C. Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding. J Chem Theory Comput 2023;19:2985-2995. [PMID: 37122117 DOI: 10.1021/acs.jctc.2c01228] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
8
Mathew AT, Baidya ATK, Das B, Devi B, Kumar R. N-glycosylation induced changes in tau protein dynamics reveal its role in tau misfolding and aggregation: A microsecond long molecular dynamics study. Proteins 2023;91:147-160. [PMID: 36029032 DOI: 10.1002/prot.26417] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/18/2022] [Accepted: 08/23/2022] [Indexed: 01/07/2023]
9
Romeo I, Ambrosio FA, Costa G, Corona A, Alkhatib M, Salpini R, Lemme S, Vergni D, Svicher V, Santoro MM, Tramontano E, Ceccherini-Silberstein F, Artese A, Alcaro S. Targeting SARS-CoV-2 nsp13 Helicase and Assessment of Druggability Pockets: Identification of Two Potent Inhibitors by a Multi-Site In Silico Drug Repurposing Approach. Molecules 2022;27:7522. [PMID: 36364347 PMCID: PMC9654784 DOI: 10.3390/molecules27217522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 06/14/2024]  Open
10
Khamaru M, Nath D, Mitra D, Roy S. Assessing Combinatorial Diversity of Aureochrome Basic Leucine Zippers through Genome-Wide Screening. Cells Tissues Organs 2022;213:133-146. [PMID: 36261029 DOI: 10.1159/000527593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]  Open
11
Yuce M, Sarica Z, Ates B, Kurkcuoglu O. Exploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow. J Biomol Struct Dyn 2022;41:3496-3510. [PMID: 35302925 DOI: 10.1080/07391102.2022.2051743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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