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For: de Brevern AG. An agnostic analysis of the human AlphaFold2 proteome using local protein conformations. Biochimie 2023;207:11-19. [PMID: 36417962 DOI: 10.1016/j.biochi.2022.11.009] [Citation(s) in RCA: 3] [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: 04/26/2022] [Revised: 10/14/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Number Cited by Other Article(s)
1
Arribas YA, Baudon B, Rotival M, Suárez G, Bonté PE, Casas V, Roubert A, Klein P, Bonnin E, Mchich B, Legoix P, Baulande S, Sadacca B, Diharce J, Waterfall JJ, Etchebest C, Carrascal M, Goudot C, Quintana-Murci L, Burbage M, Merlotti A, Amigorena S. Transposable element exonization generates a reservoir of evolving and functional protein isoforms. Cell 2024:S0092-8674(24)01328-X. [PMID: 39667937 DOI: 10.1016/j.cell.2024.11.011] [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: 06/07/2023] [Revised: 05/26/2024] [Accepted: 11/11/2024] [Indexed: 12/14/2024]
2
de Brevern AG. Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains". Int J Mol Sci 2024;25:10793. [PMID: 39409122 PMCID: PMC11477144 DOI: 10.3390/ijms251910793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 09/30/2024] [Accepted: 10/07/2024] [Indexed: 10/20/2024]  Open
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
Meuskens I, Kristiansen PE, Bardiaux B, Koynarev VR, Hatlem D, Prydz K, Lund R, Izadi-Pruneyre N, Linke D. A poly-proline II helix in YadA from Yersinia enterocolitica serotype O:9 facilitates heparin binding through electrostatic interactions. FEBS J 2024;291:761-777. [PMID: 37953437 DOI: 10.1111/febs.17001] [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: 07/14/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
5
Versini R, Sritharan S, Aykac Fas B, Tubiana T, Aimeur SZ, Henri J, Erard M, Nüsse O, Andreani J, Baaden M, Fuchs P, Galochkina T, Chatzigoulas A, Cournia Z, Santuz H, Sacquin-Mora S, Taly A. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model 2024;64:26-41. [PMID: 38124369 DOI: 10.1021/acs.jcim.3c01361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
6
Cadet F, Saavedra E, Syren PO, Gontero B. Editorial: Machine learning, epistasis, and protein engineering: From sequence-structure-function relationships to regulation of metabolic pathways. Front Mol Biosci 2022;9:1098289. [PMID: 36533069 PMCID: PMC9755881 DOI: 10.3389/fmolb.2022.1098289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/25/2022] [Indexed: 08/29/2024]  Open
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