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Number Cited by Other Article(s)
1
Fasoulis R, Rigo MM, Lizée G, Antunes DA, Kavraki LE. APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. J Chem Inf Model 2024;64:1730-1750. [PMID: 38415656 PMCID: PMC10936522 DOI: 10.1021/acs.jcim.3c01667] [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: 10/15/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
2
Liang S, Zhang C, Zhu M. Ab Initio Prediction of 3-D Conformations for Protein Long Loops with High Accuracy and Applications to Antibody CDRH3 Modeling. J Chem Inf Model 2023;63:7568-7577. [PMID: 38018130 DOI: 10.1021/acs.jcim.3c01051] [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: 11/30/2023]
3
Wang T, Wang L, Zhang X, Shen C, Zhang O, Wang J, Wu J, Jin R, Zhou D, Chen S, Liu L, Wang X, Hsieh CY, Chen G, Pan P, Kang Y, Hou T. Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. Brief Bioinform 2023;25:bbad486. [PMID: 38171930 PMCID: PMC10764206 DOI: 10.1093/bib/bbad486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]  Open
4
Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A. Architecture of the ESCPE-1 membrane coat. Nat Struct Mol Biol 2023;30:958-969. [PMID: 37322239 PMCID: PMC10352136 DOI: 10.1038/s41594-023-01014-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
5
Hernández IM, Dehouck Y, Bastolla U, López-Blanco JR, Chacón P. Predicting protein stability changes upon mutation using a simple orientational potential. Bioinformatics 2023;39:6984713. [PMID: 36629451 PMCID: PMC9850275 DOI: 10.1093/bioinformatics/btad011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/17/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023]  Open
6
Holland J, Grigoryan G. Structure‐conditioned amino‐acid couplings: how contact geometry affects pairwise sequence preferences. Protein Sci 2022;31:900-917. [PMID: 35060221 PMCID: PMC8927866 DOI: 10.1002/pro.4280] [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: 11/04/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/11/2022]
7
Bueno-Carrasco MT, Cuéllar J, Flydal MI, Santiago C, Kråkenes TA, Kleppe R, López-Blanco JR, Marcilla M, Teigen K, Alvira S, Chacón P, Martinez A, Valpuesta JM. Structural mechanism for tyrosine hydroxylase inhibition by dopamine and reactivation by Ser40 phosphorylation. Nat Commun 2022;13:74. [PMID: 35013193 PMCID: PMC8748767 DOI: 10.1038/s41467-021-27657-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/03/2021] [Indexed: 12/15/2022]  Open
8
Barozet A, Chacón P, Cortés J. Current approaches to flexible loop modeling. Curr Res Struct Biol 2021;3:187-191. [PMID: 34409304 PMCID: PMC8361254 DOI: 10.1016/j.crstbi.2021.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 06/30/2021] [Accepted: 07/25/2021] [Indexed: 01/14/2023]  Open
9
Kadukova M, Machado KDS, Chacón P, Grudinin S. KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions. Bioinformatics 2021;37:943-950. [PMID: 32840574 DOI: 10.1093/bioinformatics/btaa748] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/27/2020] [Accepted: 08/18/2020] [Indexed: 11/12/2022]  Open
10
Robustification of RosettaAntibody and Rosetta SnugDock. PLoS One 2021;16:e0234282. [PMID: 33764990 PMCID: PMC7993800 DOI: 10.1371/journal.pone.0234282] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/11/2021] [Indexed: 11/19/2022]  Open
11
Ruffolo JA, Guerra C, Mahajan SP, Sulam J, Gray JJ. Geometric potentials from deep learning improve prediction of CDR H3 loop structures. Bioinformatics 2021;36:i268-i275. [PMID: 32657412 PMCID: PMC7355305 DOI: 10.1093/bioinformatics/btaa457] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
12
Aguirre-Plans J, Meseguer A, Molina-Fernandez R, Marín-López MA, Jumde G, Casanova K, Bonet J, Fornes O, Fernandez-Fuentes N, Oliva B. SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions. BMC Bioinformatics 2021;22:4. [PMID: 33407073 PMCID: PMC7788957 DOI: 10.1186/s12859-020-03770-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/20/2020] [Indexed: 12/13/2022]  Open
13
Barozet A, Bianciotto M, Vaisset M, Siméon T, Minoux H, Cortés J. Protein loops with multiple meta-stable conformations: A challenge for sampling and scoring methods. Proteins 2020;89:218-231. [PMID: 32920900 DOI: 10.1002/prot.26008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 08/10/2020] [Accepted: 08/25/2020] [Indexed: 12/25/2022]
14
Postic G, Janel N, Tufféry P, Moroy G. An information gain-based approach for evaluating protein structure models. Comput Struct Biotechnol J 2020;18:2228-2236. [PMID: 32837711 PMCID: PMC7431362 DOI: 10.1016/j.csbj.2020.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/23/2022]  Open
15
Karami Y, Rey J, Postic G, Murail S, Tufféry P, de Vries SJ. DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Res 2020;47:W423-W428. [PMID: 31114872 PMCID: PMC6602439 DOI: 10.1093/nar/gkz403] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/20/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]  Open
16
Xu G, Wang Q, Ma J. OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling. J Chem Theory Comput 2020;16:3970-3976. [DOI: 10.1021/acs.jctc.0c00186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
17
Liu S, Xiang X, Gao X, Liu H. Neighborhood Preference of Amino Acids in Protein Structures and its Applications in Protein Structure Assessment. Sci Rep 2020;10:4371. [PMID: 32152349 PMCID: PMC7062742 DOI: 10.1038/s41598-020-61205-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 02/24/2020] [Indexed: 12/02/2022]  Open
18
Xu G, Wang Q, Ma J. OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation. J Chem Theory Comput 2020;16:1359-1366. [DOI: 10.1021/acs.jctc.9b01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
19
Serafimova K, Mihaylov I, Vassilev D, Avdjieva I, Zielenkiewicz P, Kaczanowski S. Using Machine Learning in Accuracy Assessment of Knowledge-Based Energy and Frequency Base Likelihood in Protein Structures. LECTURE NOTES IN COMPUTER SCIENCE 2020. [PMCID: PMC7304015 DOI: 10.1007/978-3-030-50420-5_43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
20
Mirzaie M. Identification of native protein structures captured by principal interactions. BMC Bioinformatics 2019;20:604. [PMID: 31752663 PMCID: PMC6873546 DOI: 10.1186/s12859-019-3186-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/01/2019] [Indexed: 11/20/2022]  Open
21
Discrimination power of knowledge-based potential dictated by the dominant energies in native protein structures. Amino Acids 2019;51:1029-1038. [PMID: 31098784 DOI: 10.1007/s00726-019-02743-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/08/2019] [Indexed: 01/20/2023]
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