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For: Xie L, Xie L, Bourne PE. A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics 2009;25:i305-12. [PMID: 19478004 PMCID: PMC2687974 DOI: 10.1093/bioinformatics/btp220] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Reim T, Ehrt C, Graef J, Günther S, Meents A, Rarey M. SiteMine: Large-scale binding site similarity searching in protein structure databases. Arch Pharm (Weinheim) 2024;357:e2300661. [PMID: 38335311 DOI: 10.1002/ardp.202300661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
2
Pallante L, Cannariato M, Androutsos L, Zizzi EA, Bompotas A, Hada X, Grasso G, Kalogeras A, Mavroudi S, Di Benedetto G, Theofilatos K, Deriu MA. VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites. Sci Rep 2024;14:6296. [PMID: 38491261 PMCID: PMC10943019 DOI: 10.1038/s41598-024-56893-7] [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: 01/09/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]  Open
3
Zhao Z, Bourne PE. How Ligands Interact with the Kinase Hinge. ACS Med Chem Lett 2023;14:1503-1508. [PMID: 37974950 PMCID: PMC10641887 DOI: 10.1021/acsmedchemlett.3c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023]  Open
4
Eguida M, Rognan D. Estimating the Similarity between Protein Pockets. Int J Mol Sci 2022;23:12462. [PMID: 36293316 PMCID: PMC9604425 DOI: 10.3390/ijms232012462] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 10/28/2023]  Open
5
Li Y, Xu Y, Yu Y. CRNNTL: Convolutional Recurrent Neural Network and Transfer Learning for QSAR Modeling in Organic Drug and Material Discovery. Molecules 2021;26:molecules26237257. [PMID: 34885843 PMCID: PMC8658888 DOI: 10.3390/molecules26237257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022]  Open
6
Bhadra A, Yeturu K. Site2Vec: a reference frame invariant algorithm for vector embedding of protein–ligand binding sites. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/abad88] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
7
Wang C, Kurgan L. Survey of Similarity-Based Prediction of Drug-Protein Interactions. Curr Med Chem 2021;27:5856-5886. [PMID: 31393241 DOI: 10.2174/0929867326666190808154841] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/16/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022]
8
Artificial intelligence in the early stages of drug discovery. Arch Biochem Biophys 2020;698:108730. [PMID: 33347838 DOI: 10.1016/j.abb.2020.108730] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
9
Lim H, He D, Qiu Y, Krawczuk P, Sun X, Xie L. Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology. PLoS Comput Biol 2019;15:e1006619. [PMID: 31206508 PMCID: PMC6576746 DOI: 10.1371/journal.pcbi.1006619] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/26/2019] [Indexed: 01/09/2023]  Open
10
Ehrt C, Brinkjost T, Koch O. Binding site characterization - similarity, promiscuity, and druggability. MEDCHEMCOMM 2019;10:1145-1159. [PMID: 31391887 DOI: 10.1039/c9md00102f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/31/2019] [Indexed: 12/19/2022]
11
Konc J. Binding site comparisons for target-centered drug discovery. Expert Opin Drug Discov 2019;14:445-454. [PMID: 30856011 DOI: 10.1080/17460441.2019.1588883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
12
Zhao Z, Xie L, Bourne PE. Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants. J Chem Inf Model 2019;59:453-462. [PMID: 30582689 DOI: 10.1021/acs.jcim.8b00458] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
13
Byrne R, Schneider G. In Silico Target Prediction for Small Molecules. Methods Mol Biol 2019;1888:273-309. [PMID: 30519953 DOI: 10.1007/978-1-4939-8891-4_16] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
14
Ehrt C, Brinkjost T, Koch O. A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs). PLoS Comput Biol 2018;14:e1006483. [PMID: 30408032 PMCID: PMC6224041 DOI: 10.1371/journal.pcbi.1006483] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 09/02/2018] [Indexed: 11/24/2022]  Open
15
Pinzi L, Caporuscio F, Rastelli G. Selection of protein conformations for structure-based polypharmacology studies. Drug Discov Today 2018;23:1889-1896. [PMID: 30099123 DOI: 10.1016/j.drudis.2018.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 11/29/2022]
16
Liu T, Ish‐Shalom S, Torng W, Lafita A, Bock C, Mort M, Cooper DN, Bliven S, Capitani G, Mooney SD, Altman RB. Biological and functional relevance of CASP predictions. Proteins 2018;86 Suppl 1:374-386. [PMID: 28975675 PMCID: PMC5820171 DOI: 10.1002/prot.25396] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/12/2017] [Accepted: 10/03/2017] [Indexed: 02/06/2023]
17
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: 0.5] [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
18
Zhao Z, Xie L, Bourne PE. Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PLoS One 2017;12:e0179936. [PMID: 28628649 PMCID: PMC5476283 DOI: 10.1371/journal.pone.0179936] [Citation(s) in RCA: 35] [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: 02/21/2017] [Accepted: 06/06/2017] [Indexed: 11/18/2022]  Open
19
Zhao Z, Liu Q, Bliven S, Xie L, Bourne PE. Determining Cysteines Available for Covalent Inhibition Across the Human Kinome. J Med Chem 2017;60:2879-2889. [PMID: 28326775 PMCID: PMC5493210 DOI: 10.1021/acs.jmedchem.6b01815] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
20
Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association. NPJ Syst Biol Appl 2016;2:16023. [PMID: 28725477 PMCID: PMC5516858 DOI: 10.1038/npjsba.2016.23] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/14/2016] [Accepted: 08/02/2016] [Indexed: 01/20/2023]  Open
21
Ehrt C, Brinkjost T, Koch O. Impact of Binding Site Comparisons on Medicinal Chemistry and Rational Molecular Design. J Med Chem 2016;59:4121-51. [PMID: 27046190 DOI: 10.1021/acs.jmedchem.6b00078] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
22
Núñez-Vivanco G, Valdés-Jiménez A, Besoaín F, Reyes-Parada M. Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach. J Cheminform 2016;8:19. [PMID: 27092185 PMCID: PMC4834829 DOI: 10.1186/s13321-016-0131-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 04/04/2016] [Indexed: 11/15/2022]  Open
23
Zhao Z, Xie L, Xie L, Bourne PE. Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach. J Med Chem 2016;59:4326-41. [PMID: 26929980 DOI: 10.1021/acs.jmedchem.5b02041] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
24
Zhao Z, Martin C, Fan R, Bourne PE, Xie L. Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology. BMC Bioinformatics 2016;17:90. [PMID: 26887654 PMCID: PMC4757998 DOI: 10.1186/s12859-016-0941-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 02/10/2016] [Indexed: 01/09/2023]  Open
25
Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L. PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics 2016;32:579-86. [PMID: 26504143 PMCID: PMC5963357 DOI: 10.1093/bioinformatics/btv597] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/24/2015] [Accepted: 10/12/2015] [Indexed: 12/31/2022]  Open
26
Liu T, Altman RB. Relating Essential Proteins to Drug Side-Effects Using Canonical Component Analysis: A Structure-Based Approach. J Chem Inf Model 2015;55:1483-94. [PMID: 26121262 DOI: 10.1021/acs.jcim.5b00030] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
27
Arooj M, Sakkiah S, Cao GP, Kim S, Arulalapperumal V, Lee KW. Finding off-targets, biological pathways, and target diseases for chymase inhibitors via structure-based systems biology approach. Proteins 2015;83:1209-24. [PMID: 25143259 DOI: 10.1002/prot.24677] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/08/2014] [Accepted: 08/14/2014] [Indexed: 02/03/2023]
28
Zhang Y, Zhao Z, Liu H. Deriving Chemically Essential Interactions Based on Active Site Alignments and Quantum Chemical Calculations: A Case Study on Glycoside Hydrolases. ACS Catal 2015. [DOI: 10.1021/cs501709d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
29
Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015;44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 258] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
30
Kaiser F, Eisold A, Labudde D. A Novel Algorithm for Enhanced Structural Motif Matching in Proteins. J Comput Biol 2015;22:698-713. [PMID: 25695840 DOI: 10.1089/cmb.2014.0263] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
31
Brylinski M. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models. PLoS Comput Biol 2014;10:e1003829. [PMID: 25232727 PMCID: PMC4168975 DOI: 10.1371/journal.pcbi.1003829] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/24/2014] [Indexed: 01/26/2023]  Open
32
Micale G, Pulvirenti A, Giugno R, Ferro A. Proteins comparison through probabilistic optimal structure local alignment. Front Genet 2014;5:302. [PMID: 25228906 PMCID: PMC4151033 DOI: 10.3389/fgene.2014.00302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 08/12/2014] [Indexed: 11/13/2022]  Open
33
Chen BY. VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials. PLoS Comput Biol 2014;10:e1003792. [PMID: 25166865 PMCID: PMC4148194 DOI: 10.1371/journal.pcbi.1003792] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/17/2014] [Indexed: 12/01/2022]  Open
34
Niu M, Hu J, Wu S, Xiaoe Z, Xu H, Zhang Y, Zhang J, Yang Y. Structural bioinformatics-based identification of EGFR inhibitor gefitinib as a putative lead compound for BACE. Chem Biol Drug Des 2014;83:81-8. [PMID: 24516878 DOI: 10.1111/cbdd.12200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
35
Chen FC, Liao YC, Huang JM, Lin CH, Chen YY, Dou HY, Hsiung CA. Pros and cons of the tuberculosis drugome approach--an empirical analysis. PLoS One 2014;9:e100829. [PMID: 24971632 PMCID: PMC4074101 DOI: 10.1371/journal.pone.0100829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/27/2014] [Indexed: 01/20/2023]  Open
36
Salentin S, Haupt VJ, Daminelli S, Schroeder M. Polypharmacology rescored: protein-ligand interaction profiles for remote binding site similarity assessment. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014;116:174-86. [PMID: 24923864 DOI: 10.1016/j.pbiomolbio.2014.05.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 05/20/2014] [Accepted: 05/26/2014] [Indexed: 11/27/2022]
37
Xie L, Ge X, Tan H, Xie L, Zhang Y, Hart T, Yang X, Bourne PE. Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol 2014;10:e1003554. [PMID: 24830652 PMCID: PMC4022462 DOI: 10.1371/journal.pcbi.1003554] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
38
Hung CL, Hua GJ. Local alignment tool based on Hadoop framework and GPU architecture. BIOMED RESEARCH INTERNATIONAL 2014;2014:541490. [PMID: 24955362 PMCID: PMC4052794 DOI: 10.1155/2014/541490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/14/2014] [Indexed: 11/17/2022]
39
Ng C, Hauptman R, Zhang Y, Bourne PE, Xie L. Anti-infectious drug repurposing using an integrated chemical genomics and structural systems biology approach. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2014:136-47. [PMID: 24297541 PMCID: PMC6322395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
40
Schumann M, Armen RS. Identification of distant drug off-targets by direct superposition of binding pocket surfaces. PLoS One 2013;8:e83533. [PMID: 24391782 PMCID: PMC3877058 DOI: 10.1371/journal.pone.0083533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/04/2013] [Indexed: 01/23/2023]  Open
41
Spitzer R, Cleves AE, Varela R, Jain AN. Protein function annotation by local binding site surface similarity. Proteins 2013;82:679-94. [PMID: 24166661 DOI: 10.1002/prot.24450] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 10/02/2013] [Accepted: 10/10/2013] [Indexed: 11/06/2022]
42
Haupt VJ, Daminelli S, Schroeder M. Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key. PLoS One 2013;8:e65894. [PMID: 23805191 PMCID: PMC3689763 DOI: 10.1371/journal.pone.0065894] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 04/30/2013] [Indexed: 11/19/2022]  Open
43
Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome. PLoS Comput Biol 2013;9:e1003087. [PMID: 23754939 PMCID: PMC3675009 DOI: 10.1371/journal.pcbi.1003087] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 04/22/2013] [Indexed: 11/22/2022]  Open
44
Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013;138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 522] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
45
Xie L, Ng C, Ali T, Valencia R, Ferreira BL, Xue V, Tanweer M, Zhou D, Haddad GG, Bourne PE, Xie L. Multiscale modeling of the causal functional roles of nsSNPs in a genome-wide association study: application to hypoxia. BMC Genomics 2013;14 Suppl 3:S9. [PMID: 23819581 PMCID: PMC3665574 DOI: 10.1186/1471-2164-14-s3-s9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]  Open
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Kirshner DA, Nilmeier JP, Lightstone FC. Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB. Nucleic Acids Res 2013;41:W256-65. [PMID: 23680785 PMCID: PMC3692059 DOI: 10.1093/nar/gkt403] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
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Hung CL, Hua GJ. Cloud computing for protein-ligand binding site comparison. BIOMED RESEARCH INTERNATIONAL 2013;2013:170356. [PMID: 23762824 PMCID: PMC3671236 DOI: 10.1155/2013/170356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/28/2013] [Indexed: 12/30/2022]
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Nilmeier JP, Kirshner DA, Wong SE, Lightstone FC. Rapid catalytic template searching as an enzyme function prediction procedure. PLoS One 2013;8:e62535. [PMID: 23675414 PMCID: PMC3651201 DOI: 10.1371/journal.pone.0062535] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/22/2013] [Indexed: 11/18/2022]  Open
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Shahid M, Shahzad Cheema M, Klenner A, Younesi E, Hofmann-Apitius M. SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling. Mol Inform 2013;32:241-9. [PMID: 27481519 DOI: 10.1002/minf.201200116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/07/2013] [Indexed: 11/10/2022]
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Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions. Structure 2013;20:1815-22. [PMID: 23141694 DOI: 10.1016/j.str.2012.09.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/14/2012] [Accepted: 09/16/2012] [Indexed: 01/12/2023]
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