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For: Brylinski M, Skolnick J. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J Comput Chem 2008;29:1574-88. [PMID: 18293308 DOI: 10.1002/jcc.20917] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Number Cited by Other Article(s)
1
Kowaguchi A, Endo K, Brumby PE, Nomura K, Yasuoka K. Optimal Replica-Exchange Molecular Simulations in Combination with Evolution Strategies. J Chem Inf Model 2022;62:6544-6552. [PMID: 35785994 DOI: 10.1021/acs.jcim.2c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
2
Skolnick J, Zhou H. Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions. J Phys Chem B 2022;126:6853-6867. [PMID: 36044742 PMCID: PMC9484464 DOI: 10.1021/acs.jpcb.2c04525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/18/2022] [Indexed: 11/28/2022]
3
Çalışkaner ZO. Computational discovery of novel inhibitory candidates targeting versatile transcriptional repressor MBD2. J Mol Model 2022;28:296. [PMID: 36066769 DOI: 10.1007/s00894-022-05297-3] [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: 04/05/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022]
4
Wang X, Hu J, Song L, Rong E, Yang C, Chen X, Pu J, Sun H, Gao C, Burt DW, Liu J, Li N, Huang Y. Functional divergence of oligoadenylate synthetase 1 (OAS1) proteins in Tetrapods. SCIENCE CHINA. LIFE SCIENCES 2022;65:1395-1412. [PMID: 34826092 DOI: 10.1007/s11427-021-2002-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
5
Assessing sequence-based protein-protein interaction predictors for use in therapeutic peptide engineering. Sci Rep 2022;12:9610. [PMID: 35688894 PMCID: PMC9187631 DOI: 10.1038/s41598-022-13227-9] [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: 10/01/2021] [Accepted: 04/25/2022] [Indexed: 12/01/2022]  Open
6
Brown BP, Vu O, Geanes AR, Kothiwale S, Butkiewicz M, Lowe EW, Mueller R, Pape R, Mendenhall J, Meiler J. Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery. Front Pharmacol 2022;13:833099. [PMID: 35264967 PMCID: PMC8899505 DOI: 10.3389/fphar.2022.833099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/24/2022] [Indexed: 01/31/2023]  Open
7
Zhou H, Cao H, Skolnick J. FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. J Chem Inf Model 2021;61:2074-2089. [PMID: 33724022 DOI: 10.1021/acs.jcim.0c01160] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
8
Paul L, Mudogo CN, Mtei KM, Machunda RL, Ntie-Kang F. A computer-based approach for developing linamarase inhibitory agents. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2019-0098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
9
Zhou H, Cao H, Skolnick J. FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. J Chem Inf Model 2018;58:2343-2354. [PMID: 30278128 PMCID: PMC6437778 DOI: 10.1021/acs.jcim.8b00309] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
10
Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking. J Comput Aided Mol Des 2018;32:769-779. [PMID: 30003468 DOI: 10.1007/s10822-018-0124-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 05/22/2018] [Indexed: 12/15/2022]
11
Assessing the similarity of ligand binding conformations with the Contact Mode Score. Comput Biol Chem 2016;64:403-413. [PMID: 27620381 DOI: 10.1016/j.compbiolchem.2016.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/17/2016] [Accepted: 08/25/2016] [Indexed: 11/22/2022]
12
Fang Y, Ding Y, Feinstein WP, Koppelman DM, Moreno J, Jarrell M, Ramanujam J, Brylinski M. GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing. PLoS One 2016;11:e0158898. [PMID: 27420300 PMCID: PMC4946785 DOI: 10.1371/journal.pone.0158898] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/23/2016] [Indexed: 12/19/2022]  Open
13
Ding Y, Fang Y, Feinstein WP, Ramanujam J, Koppelman DM, Moreno J, Brylinski M, Jarrell M. GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field. J Comput Chem 2015;36:2013-26. [PMID: 26250822 DOI: 10.1002/jcc.24031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/07/2015] [Accepted: 07/03/2015] [Indexed: 12/26/2022]
14
Brylinski M. Nonlinear Scoring Functions for Similarity-Based Ligand Docking and Binding Affinity Prediction. J Chem Inf Model 2013;53:3097-112. [DOI: 10.1021/ci400510e] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
15
Bello M, Martínez-Archundia M, Correa-Basurto J. Automated docking for novel drug discovery. Expert Opin Drug Discov 2013;8:821-34. [DOI: 10.1517/17460441.2013.794780] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
16
Skolnick J, Zhou H, Gao M. Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Curr Opin Struct Biol 2013;23:191-7. [PMID: 23415854 DOI: 10.1016/j.sbi.2013.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 01/04/2013] [Accepted: 01/23/2013] [Indexed: 01/03/2023]
17
Zhou H, Skolnick J. FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach. J Chem Inf Model 2012;53:230-40. [PMID: 23240691 DOI: 10.1021/ci300510n] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
18
Kaufmann KW, Meiler J. Using RosettaLigand for small molecule docking into comparative models. PLoS One 2012;7:e50769. [PMID: 23239984 PMCID: PMC3519832 DOI: 10.1371/journal.pone.0050769] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022]  Open
19
Carbajo D, Tramontano A. A resource for benchmarking the usefulness of protein structure models. BMC Bioinformatics 2012;13:188. [PMID: 22856649 PMCID: PMC3473236 DOI: 10.1186/1471-2105-13-188] [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: 02/19/2012] [Accepted: 07/16/2012] [Indexed: 01/13/2023]  Open
20
Zhou H, Skolnick J. FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. Mol Pharm 2012;9:1775-84. [PMID: 22574683 DOI: 10.1021/mp3000716] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
21
Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 2011;19:1108-26. [PMID: 21827947 DOI: 10.1016/j.str.2011.05.012] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/24/2011] [Accepted: 05/28/2011] [Indexed: 12/19/2022]
22
Menon R, Roy A, Mukherjee S, Belkin S, Zhang Y, Omenn GS. Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. J Proteome Res 2011;10:5503-11. [PMID: 22003824 DOI: 10.1021/pr200772w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
23
Brylinski M, Skolnick J. Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J Chem Inf Model 2011;50:1839-54. [PMID: 20853887 DOI: 10.1021/ci100235n] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
24
Brylinski M, Skolnick J. Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. Mol Pharm 2010;7:2324-33. [PMID: 20958088 DOI: 10.1021/mp1002976] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
25
Brylinski M, Lee SY, Zhou H, Skolnick J. The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. J Struct Biol 2010;173:558-69. [PMID: 20850544 DOI: 10.1016/j.jsb.2010.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 09/08/2010] [Accepted: 09/10/2010] [Indexed: 01/01/2023]
26
Huang SY, Zou X. Advances and challenges in protein-ligand docking. Int J Mol Sci 2010;11:3016-34. [PMID: 21152288 PMCID: PMC2996748 DOI: 10.3390/ijms11083016] [Citation(s) in RCA: 298] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 08/09/2010] [Accepted: 08/10/2010] [Indexed: 02/04/2023]  Open
27
Vorobjev YN. Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization. J Comput Chem 2010;31:1080-92. [PMID: 19821514 DOI: 10.1002/jcc.21394] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
28
Pierri CL, Parisi G, Porcelli V. Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010;1804:1695-712. [PMID: 20433957 DOI: 10.1016/j.bbapap.2010.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 03/04/2010] [Accepted: 04/14/2010] [Indexed: 12/12/2022]
29
Brylinski M, Skolnick J. Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J Comput Chem 2010;31:1093-105. [PMID: 19827144 PMCID: PMC2823986 DOI: 10.1002/jcc.21395] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
30
Kundrotas PJ, Vakser IA. Accuracy of protein-protein binding sites in high-throughput template-based modeling. PLoS Comput Biol 2010;6:e1000727. [PMID: 20369011 PMCID: PMC2848539 DOI: 10.1371/journal.pcbi.1000727] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 03/01/2010] [Indexed: 11/18/2022]  Open
31
Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 2010;5:725-38. [PMID: 20360767 PMCID: PMC2849174 DOI: 10.1038/nprot.2010.5] [Citation(s) in RCA: 4827] [Impact Index Per Article: 344.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
32
Zobnina V, Roterman I. Application of the fuzzy-oil-drop model to membrane protein simulation. Proteins 2009;77:378-94. [PMID: 19455711 DOI: 10.1002/prot.22443] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
33
Brylinski M, Skolnick J. FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput Biol 2009;5:e1000405. [PMID: 19503616 PMCID: PMC2685473 DOI: 10.1371/journal.pcbi.1000405] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 05/05/2009] [Indexed: 11/19/2022]  Open
34
Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009;19:145-55. [PMID: 19327982 PMCID: PMC2673339 DOI: 10.1016/j.sbi.2009.02.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 02/18/2009] [Accepted: 02/19/2009] [Indexed: 10/21/2022]
35
Skolnick J, Brylinski M. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform 2009;10:378-91. [PMID: 19324930 DOI: 10.1093/bib/bbp017] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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