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For: Regad L, Martin J, Nuel G, Camproux AC. Mining protein loops using a structural alphabet and statistical exceptionality. BMC Bioinformatics 2010;11:75. [PMID: 20132552 DOI: 10.1186/1471-2105-11-75] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 02/04/2010] [Indexed: 12/21/2022]  Open
Number Cited by Other Article(s)
1
Kumar M, Rathore RS. Disallowed spots in protein structures. Biochim Biophys Acta Gen Subj 2023;1867:130493. [PMID: 37865175 DOI: 10.1016/j.bbagen.2023.130493] [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: 05/29/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 10/23/2023]
2
Corbella M, Pinto GP, Kamerlin SCL. Loop dynamics and the evolution of enzyme activity. Nat Rev Chem 2023;7:536-547. [PMID: 37225920 DOI: 10.1038/s41570-023-00495-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2023] [Indexed: 05/26/2023]
3
Gonzalez B, Tare A, Ryu S, Johnson SC, Atzmon G, Barzilai N, Kaeberlein M, Suh Y. High-throughput sequencing analysis of nuclear-encoded mitochondrial genes reveals a genetic signature of human longevity. GeroScience 2023;45:311-330. [PMID: 35948858 PMCID: PMC9886794 DOI: 10.1007/s11357-022-00634-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/28/2022] [Indexed: 02/03/2023]  Open
4
Mitusińska K, Skalski T, Góra A. Simple Selection Procedure to Distinguish between Static and Flexible Loops. Int J Mol Sci 2020;21:ijms21072293. [PMID: 32225102 PMCID: PMC7177474 DOI: 10.3390/ijms21072293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 12/02/2022]  Open
5
SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. PLoS One 2018;13:e0198854. [PMID: 29975698 PMCID: PMC6033379 DOI: 10.1371/journal.pone.0198854] [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: 10/18/2017] [Accepted: 05/25/2018] [Indexed: 11/19/2022]  Open
6
Triki D, Cano Contreras ME, Flatters D, Visseaux B, Descamps D, Camproux AC, Regad L. Analysis of the HIV-2 protease's adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet. Sci Rep 2018;8:710. [PMID: 29335428 PMCID: PMC5768731 DOI: 10.1038/s41598-017-18941-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/18/2017] [Indexed: 12/27/2022]  Open
7
Regad L, Chéron JB, Triki D, Senac C, Flatters D, Camproux AC. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight. PLoS One 2017;12:e0182972. [PMID: 28817602 PMCID: PMC5560695 DOI: 10.1371/journal.pone.0182972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/27/2017] [Indexed: 11/18/2022]  Open
8
Bartolowits M, Davisson VJ. Considerations of Protein Subpockets in Fragment-Based Drug Design. Chem Biol Drug Des 2015;87:5-20. [PMID: 26307335 DOI: 10.1111/cbdd.12631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
9
Critical Role of a Loop at C-Terminal Domain on the Conformational Stability and Catalytic Efficiency of Chondroitinase ABC I. Mol Biotechnol 2015;57:727-34. [DOI: 10.1007/s12033-015-9864-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
10
Bonet J, Fiser A, Oliva B, Fernandez-Fuentes N. Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications. BIO-ALGORITHMS AND MED-SYSTEMS 2014. [DOI: 10.1515/bams-2014-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
11
Bonet J, Planas-Iglesias J, Garcia-Garcia J, Marín-López MA, Fernandez-Fuentes N, Oliva B. ArchDB 2014: structural classification of loops in proteins. Nucleic Acids Res 2013;42:D315-9. [PMID: 24265221 PMCID: PMC3964960 DOI: 10.1093/nar/gkt1189] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
12
Li Y. Conformational sampling in template-free protein loop structure modeling: an overview. Comput Struct Biotechnol J 2013;5:e201302003. [PMID: 24688696 PMCID: PMC3962101 DOI: 10.5936/csbj.201302003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/23/2013] [Accepted: 01/28/2013] [Indexed: 01/04/2023]  Open
13
Rorick M. Quantifying protein modularity and evolvability: a comparison of different techniques. Biosystems 2012;110:22-33. [PMID: 22796584 DOI: 10.1016/j.biosystems.2012.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/20/2012] [Accepted: 06/27/2012] [Indexed: 10/28/2022]
14
Novikova IV, Hennelly SP, Sanbonmatsu KY. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res 2012;40:5034-51. [PMID: 22362738 PMCID: PMC3367176 DOI: 10.1093/nar/gks071] [Citation(s) in RCA: 204] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
15
Ku SY, Hu YJ. Structural alphabet motif discovery and a structural motif database. Comput Biol Med 2011;42:93-105. [PMID: 22099701 DOI: 10.1016/j.compbiomed.2011.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 09/28/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
16
Regad L, Martin J, Camproux AC. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. BMC Bioinformatics 2011;12:247. [PMID: 21689388 PMCID: PMC3158783 DOI: 10.1186/1471-2105-12-247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 06/20/2011] [Indexed: 12/24/2022]  Open
17
Regad L, Saladin A, Maupetit J, Geneix C, Camproux AC. SA-Mot: a web server for the identification of motifs of interest extracted from protein loops. Nucleic Acids Res 2011;39:W203-9. [PMID: 21665924 PMCID: PMC3125790 DOI: 10.1093/nar/gkr410] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]  Open
18
Rorick MM, Wagner GP. Protein structural modularity and robustness are associated with evolvability. Genome Biol Evol 2011;3:456-75. [PMID: 21602570 PMCID: PMC3134980 DOI: 10.1093/gbe/evr046] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
19
Bastard K, Saladin A, Prévost C. Accounting for large amplitude protein deformation during in silico macromolecular docking. Int J Mol Sci 2011;12:1316-33. [PMID: 21541061 PMCID: PMC3083708 DOI: 10.3390/ijms12021316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/07/2011] [Accepted: 02/08/2011] [Indexed: 12/23/2022]  Open
20
Baussand J, Camproux AC. Deciphering the shape and deformation of secondary structures through local conformation analysis. BMC STRUCTURAL BIOLOGY 2011;11:9. [PMID: 21284872 PMCID: PMC3224362 DOI: 10.1186/1472-6807-11-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 02/01/2011] [Indexed: 12/30/2022]
21
Hirani TA, Tovar-Méndez A, Miernyk JA, Randall DD. Asp295 stabilizes the active-site loop structure of pyruvate dehydrogenase, facilitating phosphorylation of ser292 by pyruvate dehydrogenase-kinase. Enzyme Res 2011;2011:939068. [PMID: 21318135 PMCID: PMC3034952 DOI: 10.4061/2011/939068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 11/05/2010] [Indexed: 01/22/2023]  Open
22
Totrov M. Loop simulations. Methods Mol Biol 2011;857:207-29. [PMID: 22323223 DOI: 10.1007/978-1-61779-588-6_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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