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For: Lee HS, Im W. Identification of ligand templates using local structure alignment for structure-based drug design. J Chem Inf Model 2012;52:2784-95. [PMID: 22978550 DOI: 10.1021/ci300178e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Guterres H, Park SJ, Cao Y, Im W. CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site. J Chem Inf Model 2021;61:5336-5342. [PMID: 34757752 DOI: 10.1021/acs.jcim.1c01156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
2
Guterres H, Park SJ, Zhang H, Im W. CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement. J Chem Inf Model 2021;61:3744-3751. [PMID: 34296608 DOI: 10.1021/acs.jcim.1c00561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
3
Guterres H, Park SJ, Jiang W, Im W. Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. J Chem Inf Model 2020;61:535-546. [PMID: 33337877 DOI: 10.1021/acs.jcim.0c01354] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
4
Cao Y, Park SJ, Im W. A systematic analysis of protein-carbohydrate interactions in the Protein Data Bank. Glycobiology 2020;31:126-136. [PMID: 32614943 DOI: 10.1093/glycob/cwaa062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022]  Open
5
Profiling the Protein Targets of Unmodified Bio‐Active Molecules with Drug Affinity Responsive Target Stability and Liquid Chromatography/Tandem Mass Spectrometry. Proteomics 2020;20:e1900325. [DOI: 10.1002/pmic.201900325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/28/2019] [Indexed: 12/17/2022]
6
Guterres H, Lee HS, Im W. Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates. J Chem Theory Comput 2019;15:6524-6535. [PMID: 31557013 DOI: 10.1021/acs.jctc.9b00751] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
7
Lee HS, Im W. Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. J Comput Chem 2019;40:1622-1632. [PMID: 30829435 DOI: 10.1002/jcc.25813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/23/2019] [Accepted: 02/17/2019] [Indexed: 12/20/2022]
8
Lee HS, Im W. G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures. Methods Mol Biol 2018;1611:97-108. [PMID: 28451974 DOI: 10.1007/978-1-4939-7015-5_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
9
Raškevičius V, Mikalayeva V, Antanavičiūtė I, Ceslevičienė I, Skeberdis VA, Kairys V, Bordel S. Genome scale metabolic models as tools for drug design and personalized medicine. PLoS One 2018;13:e0190636. [PMID: 29304175 PMCID: PMC5755790 DOI: 10.1371/journal.pone.0190636] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/18/2017] [Indexed: 01/03/2023]  Open
10
Lee J, Konc J, Janežič D, Brooks BR. Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. Sci Rep 2017;7:11652. [PMID: 28912495 PMCID: PMC5599562 DOI: 10.1038/s41598-017-10412-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/07/2017] [Indexed: 01/06/2023]  Open
11
Lee HS, Im W. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design. Protein Sci 2016;25:865-76. [PMID: 26813336 DOI: 10.1002/pro.2890] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 11/11/2022]
12
Shin WH, Bures MG, Kihara D. PatchSurfers: Two methods for local molecular property-based binding ligand prediction. Methods 2016;93:41-50. [PMID: 26427548 PMCID: PMC4718779 DOI: 10.1016/j.ymeth.2015.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/27/2015] [Accepted: 09/28/2015] [Indexed: 01/09/2023]  Open
13
Konc J, Miller BT, Štular T, Lešnik S, Woodcock HL, Brooks BR, Janežič D. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J Chem Inf Model 2015;55:2308-14. [DOI: 10.1021/acs.jcim.5b00534] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
14
Modeling enzyme-ligand binding in drug discovery. J Cheminform 2015;7:48. [PMID: 26457119 PMCID: PMC4594084 DOI: 10.1186/s13321-015-0096-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/29/2015] [Indexed: 01/09/2023]  Open
15
Bartolowits M, Davisson VJ. Considerations of Protein Subpockets in Fragment-Based Drug Design. Chem Biol Drug Des 2015;87:5-20. [PMID: 26307335 DOI: 10.1111/cbdd.12631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
16
Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W. GS-align for glycan structure alignment and similarity measurement. Bioinformatics 2015;31:2653-9. [PMID: 25857669 DOI: 10.1093/bioinformatics/btv202] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/03/2015] [Indexed: 11/13/2022]  Open
17
Konc J, Janežič D. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites. Nucleic Acids Res 2014;42:W215-20. [PMID: 24861616 PMCID: PMC4086080 DOI: 10.1093/nar/gku460] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]  Open
18
Konc J, Janežič D. Binding site comparison for function prediction and pharmaceutical discovery. Curr Opin Struct Biol 2013;25:34-9. [PMID: 24878342 DOI: 10.1016/j.sbi.2013.11.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 11/30/2022]
19
Lee HS, Im W. Ligand binding site detection by local structure alignment and its performance complementarity. J Chem Inf Model 2013;53:2462-70. [PMID: 23957286 DOI: 10.1021/ci4003602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
20
Murakami Y, Kinoshita K, Kinjo AR, Nakamura H. Exhaustive comparison and classification of ligand-binding surfaces in proteins. Protein Sci 2013;22:1379-91. [PMID: 23934772 PMCID: PMC3795496 DOI: 10.1002/pro.2329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/29/2013] [Accepted: 08/05/2013] [Indexed: 12/03/2022]
21
Topham CM, Rouquier M, Tarrat N, André I. Adaptive Smith-Waterman residue match seeding for protein structural alignment. Proteins 2013;81:1823-39. [DOI: 10.1002/prot.24327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/22/2013] [Accepted: 05/15/2013] [Indexed: 12/30/2022]
22
Jo S, Lee HS, Skolnick J, Im W. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol 2013;9:e1002946. [PMID: 23516343 PMCID: PMC3597548 DOI: 10.1371/journal.pcbi.1002946] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/10/2013] [Indexed: 11/29/2022]  Open
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