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For: Lensink MF, Wodak SJ. Score_set: A CAPRI benchmark for scoring protein complexes. Proteins 2014;82:3163-9. [DOI: 10.1002/prot.24678] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/05/2014] [Accepted: 08/22/2014] [Indexed: 12/26/2022]
Number Cited by Other Article(s)
1
Le HN, de Freitas MV, Antunes DA. Strengths and limitations of web servers for the modeling of TCRpMHC complexes. Comput Struct Biotechnol J 2024;23:2938-2948. [PMID: 39104710 PMCID: PMC11298609 DOI: 10.1016/j.csbj.2024.06.028] [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: 03/31/2024] [Revised: 06/22/2024] [Accepted: 06/23/2024] [Indexed: 08/07/2024]  Open
2
Yang Q, Jin X, Zhou H, Ying J, Zou J, Liao Y, Lu X, Ge S, Yu H, Min X. SurfPro-NN: A 3D point cloud neural network for the scoring of protein-protein docking models based on surfaces features and protein language models. Comput Biol Chem 2024;110:108067. [PMID: 38714420 DOI: 10.1016/j.compbiolchem.2024.108067] [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: 01/18/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024]
3
Tomezsko PJ, Ford CT, Meyer AE, Michaleas AM, Jaimes R. Human cytokine and coronavirus nucleocapsid protein interactivity using large-scale virtual screens. FRONTIERS IN BIOINFORMATICS 2024;4:1397968. [PMID: 38855143 PMCID: PMC11157076 DOI: 10.3389/fbinf.2024.1397968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/26/2024] [Indexed: 06/11/2024]  Open
4
Zhao H, Petrey D, Murray D, Honig B. ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models. Proc Natl Acad Sci U S A 2024;121:e2400260121. [PMID: 38743624 PMCID: PMC11127014 DOI: 10.1073/pnas.2400260121] [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: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024]  Open
5
Chen X, Liu J, Park N, Cheng J. A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models. Biomolecules 2024;14:574. [PMID: 38785981 PMCID: PMC11117562 DOI: 10.3390/biom14050574] [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: 03/01/2024] [Revised: 04/07/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]  Open
6
Ovek D, Keskin O, Gursoy A. ProInterVal: Validation of Protein-Protein Interfaces through Learned Interface Representations. J Chem Inf Model 2024;64:2979-2987. [PMID: 38526504 PMCID: PMC11040718 DOI: 10.1021/acs.jcim.3c01788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024]
7
McCoy KM, Ackerman ME, Grigoryan G. A significance score for protein-protein interaction models through random docking. Protein Sci 2024;33:e4853. [PMID: 38078680 PMCID: PMC10806930 DOI: 10.1002/pro.4853] [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: 06/23/2023] [Revised: 10/26/2023] [Accepted: 12/02/2023] [Indexed: 01/27/2024]
8
Xu X, Bonvin AMJJ. DeepRank-GNN-esm: a graph neural network for scoring protein-protein models using protein language model. BIOINFORMATICS ADVANCES 2024;4:vbad191. [PMID: 38213822 PMCID: PMC10782804 DOI: 10.1093/bioadv/vbad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/19/2023] [Indexed: 01/13/2024]
9
Zhang L, Wang S, Hou J, Si D, Zhu J, Cao R. ComplexQA: a deep graph learning approach for protein complex structure assessment. Brief Bioinform 2023;24:bbad287. [PMID: 37930021 DOI: 10.1093/bib/bbad287] [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: 02/24/2023] [Revised: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 11/07/2023]  Open
10
Schweke H, Xu Q, Tauriello G, Pantolini L, Schwede T, Cazals F, Lhéritier A, Fernandez-Recio J, Rodríguez-Lumbreras LÁ, Schueler-Furman O, Varga JK, Jiménez-García B, Réau MF, Bonvin A, Savojardo C, Martelli PL, Casadio R, Tubiana J, Wolfson H, Oliva R, Barradas-Bautista D, Ricciardelli T, Cavallo L, Venclovas Č, Olechnovič K, Guerois R, Andreani J, Martin J, Wang X, Kihara D, Marchand A, Correia B, Zou X, Dey S, Dunbrack R, Levy E, Wodak S. Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics 2023;23:e2200323. [PMID: 37365936 PMCID: PMC10937251 DOI: 10.1002/pmic.202200323] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/28/2023]
11
Chen Z, Liu N, Huang Y, Min X, Zeng X, Ge S, Zhang J, Xia N. PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023;20:3128-3138. [PMID: 37220029 DOI: 10.1109/tcbb.2023.3279019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
12
Chen X, Morehead A, Liu J, Cheng J. A gated graph transformer for protein complex structure quality assessment and its performance in CASP15. Bioinformatics 2023;39:i308-i317. [PMID: 37387159 PMCID: PMC10311325 DOI: 10.1093/bioinformatics/btad203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
13
McFee M, Kim PM. GDockScore: a graph-based protein-protein docking scoring function. BIOINFORMATICS ADVANCES 2023;3:vbad072. [PMID: 37359726 PMCID: PMC10290236 DOI: 10.1093/bioadv/vbad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/30/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
14
Wodak SJ, Vajda S, Lensink MF, Kozakov D, Bates PA. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes. Annu Rev Biophys 2023;52:183-206. [PMID: 36626764 PMCID: PMC10885158 DOI: 10.1146/annurev-biophys-102622-084607] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
15
Kim HY, Kim S, Park WY, Kim D. G-RANK: an equivariant graph neural network for the scoring of protein-protein docking models. BIOINFORMATICS ADVANCES 2023;3:vbad011. [PMID: 36818727 PMCID: PMC9927558 DOI: 10.1093/bioadv/vbad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
16
Jung Y, Geng C, Bonvin AMJJ, Xue LC, Honavar VG. MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 2023;13:121. [PMID: 36671507 PMCID: PMC9855734 DOI: 10.3390/biom13010121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023]  Open
17
Nagaraju M, Liu H. A scoring function for the prediction of protein complex interfaces based on the neighborhood preferences of amino acids. Acta Crystallogr D Struct Biol 2023;79:31-39. [PMID: 36601805 DOI: 10.1107/s2059798322011858] [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: 05/18/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]  Open
18
Réau M, Renaud N, Xue LC, Bonvin AMJJ. DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces. Bioinformatics 2022;39:6845451. [PMID: 36420989 PMCID: PMC9805592 DOI: 10.1093/bioinformatics/btac759] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 10/19/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]  Open
19
Xu T, Zhu K, Beautrait A, Vendome J, Borrelli KW, Abel R, Friesner RA, Miller EB. Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models. J Chem Theory Comput 2022;18:5710-5724. [PMID: 35972903 DOI: 10.1021/acs.jctc.2c00371] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Pozzati G, Kundrotas P, Elofsson A. Scoring of protein–protein docking models utilizing predicted interface residues. Proteins 2022;90:1493-1505. [PMID: 35246997 PMCID: PMC9314140 DOI: 10.1002/prot.26330] [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: 08/27/2021] [Revised: 02/23/2022] [Accepted: 02/28/2022] [Indexed: 11/08/2022]
21
Kotthoff I, Kundrotas PJ, Vakser IA. Dockground scoring benchmarks for protein docking. Proteins 2022;90:1259-1266. [DOI: 10.1002/prot.26306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/06/2021] [Accepted: 01/21/2022] [Indexed: 11/05/2022]
22
Mahita J, Kim DG, Son S, Choi Y, Kim HS, Bailey-Kellogg C. Computational epitope binning reveals functional equivalence of sequence-divergent paratopes. Comput Struct Biotechnol J 2022;20:2169-2180. [PMID: 35615020 PMCID: PMC9118127 DOI: 10.1016/j.csbj.2022.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/26/2022]  Open
23
Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein–Protein Interfaces, How and Why? Molecules 2022;27:molecules27061841. [PMID: 35335203 PMCID: PMC8950966 DOI: 10.3390/molecules27061841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/07/2022]  Open
24
Hippe K, Lilley C, William Berkenpas J, Chandana Pocha C, Kishaba K, Ding H, Hou J, Si D, Cao R. ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features. Brief Bioinform 2022;23:bbab384. [PMID: 34553747 PMCID: PMC8499977 DOI: 10.1093/bib/bbab384] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/02/2021] [Accepted: 08/28/2021] [Indexed: 12/13/2022]  Open
25
Renaud N, Geng C, Georgievska S, Ambrosetti F, Ridder L, Marzella DF, Réau MF, Bonvin AMJJ, Xue LC. DeepRank: a deep learning framework for data mining 3D protein-protein interfaces. Nat Commun 2021;12:7068. [PMID: 34862392 PMCID: PMC8642403 DOI: 10.1038/s41467-021-27396-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]  Open
26
Jandova Z, Vargiu AV, Bonvin AMJJ. Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue. J Chem Theory Comput 2021;17:5944-5954. [PMID: 34342983 PMCID: PMC8444332 DOI: 10.1021/acs.jctc.1c00336] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 11/29/2022]
27
Prévost C, Sacquin-Mora S. Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces. Proteins 2021;89:1315-1323. [PMID: 34038009 DOI: 10.1002/prot.26152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/22/2021] [Accepted: 05/19/2021] [Indexed: 11/06/2022]
28
Wang X, Flannery ST, Kihara D. Protein Docking Model Evaluation by Graph Neural Networks. Front Mol Biosci 2021;8:647915. [PMID: 34113650 PMCID: PMC8185212 DOI: 10.3389/fmolb.2021.647915] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/26/2021] [Indexed: 12/03/2022]  Open
29
Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021;12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023]  Open
30
McCafferty CL, Marcotte EM, Taylor DW. Simplified geometric representations of protein structures identify complementary interaction interfaces. Proteins 2021;89:348-360. [PMID: 33140424 PMCID: PMC7855953 DOI: 10.1002/prot.26020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/22/2020] [Accepted: 10/25/2020] [Indexed: 12/12/2022]
31
Rosário-Ferreira N, Marques-Pereira C, Gouveia RP, Mourão J, Moreira IS. Guardians of the Cell: State-of-the-Art of Membrane Proteins from a Computational Point-of-View. Methods Mol Biol 2021;2315:3-28. [PMID: 34302667 DOI: 10.1007/978-1-0716-1468-6_1] [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: 01/06/2023]
32
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: 2.8] [Reference Citation Analysis] [Abstract] [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
33
Integrative modeling of membrane-associated protein assemblies. Nat Commun 2020;11:6210. [PMID: 33277503 PMCID: PMC7718903 DOI: 10.1038/s41467-020-20076-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/13/2020] [Indexed: 01/03/2023]  Open
34
Roy AA, Dhawanjewar AS, Sharma P, Singh G, Madhusudhan MS. Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions. Nucleic Acids Res 2020;47:W331-W337. [PMID: 31114890 PMCID: PMC6602501 DOI: 10.1093/nar/gkz368] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/24/2019] [Accepted: 05/15/2019] [Indexed: 11/24/2022]  Open
35
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Res 2020;9. [PMID: 32566135 PMCID: PMC7284151 DOI: 10.12688/f1000research.20559.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2020] [Indexed: 12/11/2022]  Open
36
Cao Y, Shen Y. Energy-based graph convolutional networks for scoring protein docking models. Proteins 2020;88:1091-1099. [PMID: 32144844 DOI: 10.1002/prot.25888] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/15/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022]
37
Kundrotas PJ, Kotthoff I, Choi SW, Copeland MM, Vakser IA. Dockground Tool for Development and Benchmarking of Protein Docking Procedures. Methods Mol Biol 2020;2165:289-300. [PMID: 32621232 DOI: 10.1007/978-1-0716-0708-4_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
38
Geng C, Jung Y, Renaud N, Honavar V, Bonvin AMJJ, Xue LC. iScore: a novel graph kernel-based function for scoring protein-protein docking models. Bioinformatics 2020;36:112-121. [PMID: 31199455 PMCID: PMC6956772 DOI: 10.1093/bioinformatics/btz496] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/08/2019] [Accepted: 06/11/2019] [Indexed: 11/12/2022]  Open
39
Renaud N, Jung Y, Honavar V, Geng C, Bonvin AM, Xue LC. iScore: An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines. SOFTWAREX 2020;11:100462. [PMID: 35419466 PMCID: PMC9005067 DOI: 10.1016/j.softx.2020.100462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
40
Perthold JW, Oostenbrink C. GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations. J Chem Inf Model 2019;59:5074-5085. [DOI: 10.1021/acs.jcim.9b00687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
41
Pfeiffenberger E, Bates PA. Refinement of protein-protein complexes in contact map space with metadynamics simulations. Proteins 2019;87:12-22. [PMID: 30370948 PMCID: PMC6492248 DOI: 10.1002/prot.25612] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 09/21/2018] [Accepted: 09/26/2018] [Indexed: 12/18/2022]
42
Development of a new benchmark for assessing the scoring functions applicable to protein–protein interactions. Future Med Chem 2018;10:1555-1574. [DOI: 10.4155/fmc-2017-0261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
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Gaines JC, Acebes S, Virrueta A, Butler M, Regan L, O'Hern CS. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Proteins 2018;86:581-591. [PMID: 29427530 PMCID: PMC5912992 DOI: 10.1002/prot.25479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/06/2018] [Indexed: 12/26/2022]
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Simões ICM, Coimbra JTS, Neves RPP, Costa IPD, Ramos MJ, Fernandes PA. Properties that rank protein:protein docking poses with high accuracy. Phys Chem Chem Phys 2018;20:20927-20942. [DOI: 10.1039/c8cp03888k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Barradas-Bautista D, Rosell M, Pallara C, Fernández-Recio J. Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems. PROTEIN-PROTEIN INTERACTIONS IN HUMAN DISEASE, PART A 2018;110:203-249. [DOI: 10.1016/bs.apcsb.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Kundrotas PJ, Anishchenko I, Dauzhenka T, Kotthoff I, Mnevets D, Copeland MM, Vakser IA. Dockground: A comprehensive data resource for modeling of protein complexes. Protein Sci 2017;27:172-181. [PMID: 28891124 DOI: 10.1002/pro.3295] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/28/2022]
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Basu S, Wallner B. Finding correct protein-protein docking models using ProQDock. Bioinformatics 2017;32:i262-i270. [PMID: 27307625 PMCID: PMC4908341 DOI: 10.1093/bioinformatics/btw257] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
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Barradas-Bautista D, Moal IH, Fernández-Recio J. A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining. Proteins 2017;85:1287-1297. [DOI: 10.1002/prot.25289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/08/2017] [Accepted: 03/20/2017] [Indexed: 12/24/2022]
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Pfeiffenberger E, Chaleil RA, Moal IH, Bates PA. A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison. Proteins 2017;85:528-543. [PMID: 27935158 PMCID: PMC5396268 DOI: 10.1002/prot.25218] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 01/28/2023]
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Gromiha MM, Yugandhar K, Jemimah S. Protein-protein interactions: scoring schemes and binding affinity. Curr Opin Struct Biol 2016;44:31-38. [PMID: 27866112 DOI: 10.1016/j.sbi.2016.10.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/30/2016] [Accepted: 10/25/2016] [Indexed: 01/16/2023]
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