• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4597351)   Today's Articles (5544)   Subscriber (49348)
For: Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins 2011;78:3111-4. [PMID: 20806234 DOI: 10.1002/prot.22830] [Citation(s) in RCA: 350] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Number Cited by Other Article(s)
1
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]
2
Su Z, Dhusia K, Wu Y. Encoding the space of protein-protein binding interfaces by artificial intelligence. Comput Biol Chem 2024;110:108080. [PMID: 38643609 DOI: 10.1016/j.compbiolchem.2024.108080] [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: 12/15/2023] [Revised: 04/03/2024] [Accepted: 04/17/2024] [Indexed: 04/23/2024]
3
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
4
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 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] [Indexed: 03/26/2024]
5
Zhao N, Han B, Zhao C, Xu J, Gong X. ABAG-docking benchmark: a non-redundant structure benchmark dataset for antibody-antigen computational docking. Brief Bioinform 2024;25:bbae048. [PMID: 38385879 PMCID: PMC10883643 DOI: 10.1093/bib/bbae048] [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: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 02/23/2024]  Open
6
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: 4] [Impact Index Per Article: 4.0] [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]
7
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]
8
Will I, Beckerson WC, de Bekker C. Using machine learning to predict protein-protein interactions between a zombie ant fungus and its carpenter ant host. Sci Rep 2023;13:13821. [PMID: 37620441 PMCID: PMC10449854 DOI: 10.1038/s41598-023-40764-8] [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: 01/06/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]  Open
9
Yang L, Guo S, Liao C, Hou C, Jiang S, Li J, Ma X, Shi L, Ye L, He X. Spatial Layouts of Low-Entropy Hydration Shells Guide Protein Binding. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023;7:2300022. [PMID: 37483413 PMCID: PMC10362119 DOI: 10.1002/gch2.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/29/2023] [Indexed: 07/25/2023]
10
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]
11
Shuvo MH, Karim M, Roche R, Bhattacharya D. PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries. BIOINFORMATICS ADVANCES 2023;3:vbad070. [PMID: 37351310 PMCID: PMC10281963 DOI: 10.1093/bioadv/vbad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/17/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023]
12
Rui H, Ashton KS, Min J, Wang C, Potts PR. Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction. RSC Chem Biol 2023;4:192-215. [PMID: 36908699 PMCID: PMC9994104 DOI: 10.1039/d2cb00207h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023]  Open
13
Ebola virus disease: In vivo protection provided by the PAMP restricted TLR3 agonist rintatolimod and its mechanism of action. Antiviral Res 2023;212:105554. [PMID: 36804324 DOI: 10.1016/j.antiviral.2023.105554] [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] [Received: 11/22/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023]
14
PIQLE: protein-protein interface quality estimation by deep graph learning of multimeric interaction geometries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528528. [PMID: 36824789 PMCID: PMC9949034 DOI: 10.1101/2023.02.14.528528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
15
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
16
Increased slow dynamics defines ligandability of BTB domains. Nat Commun 2022;13:6989. [PMID: 36384931 PMCID: PMC9668832 DOI: 10.1038/s41467-022-34599-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]  Open
17
Martin J, Frezza E. A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations. Front Mol Biosci 2022;9:970109. [PMID: 36275619 PMCID: PMC9583002 DOI: 10.3389/fmolb.2022.970109] [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: 06/15/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022]  Open
18
Li Y, Song J, Zhou P, Zhou J, Xie S. Targeting Undruggable Transcription Factors with PROTACs: Advances and Perspectives. J Med Chem 2022;65:10183-10194. [PMID: 35881047 DOI: 10.1021/acs.jmedchem.2c00691] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
Hurwitz N, Zaidman D, Wolfson HJ. Pep–Whisperer: Inhibitory peptide design. Proteins 2022;90:1886-1895. [DOI: 10.1002/prot.26384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/07/2022]
20
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]
21
Casadio R, Martelli PL, Savojardo C. Machine learning solutions for predicting protein–protein interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
22
Guo L, He J, Lin P, Huang SY, Wang J. TRScore: a three-dimensional RepVGG-based scoring method for ranking protein docking models. Bioinformatics 2022;38:2444-2451. [PMID: 35199137 DOI: 10.1093/bioinformatics/btac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/19/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022]  Open
23
Li S, Wu S, Wang L, Li F, Jiang H, Bai F. Recent advances in predicting protein-protein interactions with the aid of artificial intelligence algorithms. Curr Opin Struct Biol 2022;73:102344. [PMID: 35219216 DOI: 10.1016/j.sbi.2022.102344] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 12/15/2022]
24
Myung Y, Pires DEV, Ascher DB. CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function. Bioinformatics 2022;38:1141-1143. [PMID: 34734992 DOI: 10.1093/bioinformatics/btab762] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/18/2021] [Accepted: 11/01/2021] [Indexed: 02/03/2023]  Open
25
Li H, Yan Y, Zhao X, Huang SY. Inclusion of Desolvation Energy into Protein–Protein Docking through Atomic Contact Potentials. J Chem Inf Model 2022;62:740-750. [DOI: 10.1021/acs.jcim.1c01483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
26
PEPscan: A Broad Spectrum Approach for the Characterization of Protein-Binder Interactions? Biomolecules 2022;12:biom12020178. [PMID: 35204680 PMCID: PMC8961561 DOI: 10.3390/biom12020178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 01/25/2023]  Open
27
Aschmann D, Vallet C, Tripathi SK, Ruiz‐Blanco YB, Brabender M, Schmuck C, Sanchez‐Garcia E, Knauer SK, Giese M. Selective Disruption of Survivin's Protein‐Protein Interactions: A Supramolecular Approach Based on Guanidiniocarbonylpyrrole. Chembiochem 2022;23:e202100618. [PMID: 35043526 PMCID: PMC9303230 DOI: 10.1002/cbic.202100618] [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: 11/09/2021] [Revised: 12/09/2021] [Indexed: 11/20/2022]
28
Barradas-Bautista D, Cao Z, Vangone A, Oliva R, Cavallo L. A random forest classifier for protein-protein docking models. BIOINFORMATICS ADVANCES 2021;2:vbab042. [PMID: 36699405 PMCID: PMC9710594 DOI: 10.1093/bioadv/vbab042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/11/2021] [Accepted: 12/06/2021] [Indexed: 01/28/2023]
29
Protein-Protein Docking: Past, Present, and Future. Protein J 2021;41:1-26. [PMID: 34787783 DOI: 10.1007/s10930-021-10031-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 10/19/2022]
30
Weng G, Li D, Kang Y, Hou T. Integrative Modeling of PROTAC-Mediated Ternary Complexes. J Med Chem 2021;64:16271-16281. [PMID: 34709816 DOI: 10.1021/acs.jmedchem.1c01576] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
31
Soltanikazemi E, Quadir F, Roy RS, Guo Z, Cheng J. Distance-based reconstruction of protein quaternary structures from inter-chain contacts. Proteins 2021;90:720-731. [PMID: 34716620 PMCID: PMC8816881 DOI: 10.1002/prot.26269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/25/2021] [Accepted: 10/12/2021] [Indexed: 12/21/2022]
32
Perera DDBD, Perera KML, Peiris DC. A Novel In Silico Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery. BIOLOGY 2021;10:biology10111113. [PMID: 34827106 PMCID: PMC8615085 DOI: 10.3390/biology10111113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/16/2021] [Accepted: 10/25/2021] [Indexed: 01/11/2023]
33
Sledzieski S, Singh R, Cowen L, Berger B. D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Syst 2021;12:969-982.e6. [PMID: 34536380 PMCID: PMC8586911 DOI: 10.1016/j.cels.2021.08.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/01/2021] [Accepted: 08/19/2021] [Indexed: 11/29/2022]
34
Mias-Lucquin D, Chauvot de Beauchene I. Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives. Proteins 2021;90:625-631. [PMID: 34617336 PMCID: PMC9292434 DOI: 10.1002/prot.26258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022]
35
Quadir F, Roy RS, Soltanikazemi E, Cheng J. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling. Front Mol Biosci 2021;8:716973. [PMID: 34497831 PMCID: PMC8419425 DOI: 10.3389/fmolb.2021.716973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022]  Open
36
Han Y, He F, Chen Y, Qin W, Yu H, Xu D. Quality Assessment of Protein Docking Models Based on Graph Neural Network. FRONTIERS IN BIOINFORMATICS 2021;1:693211. [PMID: 36303780 PMCID: PMC9581034 DOI: 10.3389/fbinf.2021.693211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]  Open
37
Panchal D, Kataria J, Patel K, Crowe K, Pai V, Azizogli AR, Kadian N, Sanyal S, Roy A, Dodd-O J, Acevedo-Jake AM, Kumar VA. Peptide-Based Inhibitors for SARS-CoV-2 and SARS-CoV. ADVANCED THERAPEUTICS 2021;4:2100104. [PMID: 34514085 PMCID: PMC8420164 DOI: 10.1002/adtp.202100104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/14/2021] [Indexed: 12/20/2022]
38
van Noort CW, Honorato RV, Bonvin AMJJ. Information-driven modeling of biomolecular complexes. Curr Opin Struct Biol 2021;70:70-77. [PMID: 34139639 DOI: 10.1016/j.sbi.2021.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2021] [Indexed: 11/15/2022]
39
Peacock T, Chain B. Information-Driven Docking for TCR-pMHC Complex Prediction. Front Immunol 2021;12:686127. [PMID: 34177934 PMCID: PMC8219952 DOI: 10.3389/fimmu.2021.686127] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/07/2021] [Indexed: 12/16/2022]  Open
40
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: 22] [Impact Index Per Article: 7.3] [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
41
Liang T, Chen H, Yuan J, Jiang C, Hao Y, Wang Y, Feng Z, Xie XQ. IsAb: a computational protocol for antibody design. Brief Bioinform 2021;22:6238584. [PMID: 33876197 DOI: 10.1093/bib/bbab143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/24/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022]  Open
42
Sotudian S, Desta IT, Hashemi N, Zarbafian S, Kozakov D, Vakili P, Vajda S, Paschalidis IC. Improved cluster ranking in protein-protein docking using a regression approach. Comput Struct Biotechnol J 2021;19:2269-2278. [PMID: 33995918 PMCID: PMC8102165 DOI: 10.1016/j.csbj.2021.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 11/21/2022]  Open
43
Ueda T, Tamura T, Kawano M, Shiono K, Hobor F, Wilson AJ, Hamachi I. Enhanced Suppression of a Protein–Protein Interaction in Cells Using Small-Molecule Covalent Inhibitors Based on an N-Acyl-N-alkyl Sulfonamide Warhead. J Am Chem Soc 2021;143:4766-4774. [DOI: 10.1021/jacs.1c00703] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
44
Pattern Discovery and Disentanglement for Aligned Pattern Cluster Analysis and Protein Binding Complexes Detection. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]  Open
45
Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG. An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure 2021;29:606-621.e5. [PMID: 33539768 DOI: 10.1016/j.str.2021.01.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 11/15/2020] [Accepted: 01/11/2021] [Indexed: 01/04/2023]
46
Slater O, Miller B, Kontoyianni M. Decoding Protein-protein Interactions: An Overview. Curr Top Med Chem 2021;20:855-882. [PMID: 32101126 DOI: 10.2174/1568026620666200226105312] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 11/27/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022]
47
Eismann S, Townshend RJL, Thomas N, Jagota M, Jing B, Dror RO. Hierarchical, rotation-equivariant neural networks to select structural models of protein complexes. Proteins 2020;89:493-501. [PMID: 33289162 DOI: 10.1002/prot.26033] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 10/10/2020] [Accepted: 11/21/2020] [Indexed: 12/16/2022]
48
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
49
Algar S, Martín-Martínez M, González-Muñiz R. Evolution in non-peptide α-helix mimetics on the road to effective protein-protein interaction modulators. Eur J Med Chem 2020;211:113015. [PMID: 33423841 DOI: 10.1016/j.ejmech.2020.113015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023]
50
Launay G, Ohue M, Prieto Santero J, Matsuzaki Y, Hilpert C, Uchikoga N, Hayashi T, Martin J. Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses. Front Mol Biosci 2020;7:559005. [PMID: 33195406 PMCID: PMC7641601 DOI: 10.3389/fmolb.2020.559005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022]  Open
PrevPage 1 of 7 1234567Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA