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For: Tang GW, Altman RB. Knowledge-based fragment binding prediction. PLoS Comput Biol 2014;10:e1003589. [PMID: 24762971 PMCID: PMC3998881 DOI: 10.1371/journal.pcbi.1003589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 03/11/2014] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Chandraghatgi R, Ji HF, Rosen GL, Sokhansanj BA. Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening. J Chem Inf Model 2024;64:3826-3840. [PMID: 38696451 PMCID: PMC11197033 DOI: 10.1021/acs.jcim.4c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/04/2024]
2
Wilson J, Sokhansanj BA, Chong WC, Chandraghatgi R, Rosen GL, Ji HF. Fragment databases from screened ligands for drug discovery (FDSL-DD). J Mol Graph Model 2024;127:108669. [PMID: 38011826 DOI: 10.1016/j.jmgm.2023.108669] [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: 09/14/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023]
3
Bryan DR, Kulp JL, Mahapatra MK, Bryan RL, Viswanathan U, Carlisle MN, Kim S, Schutte WD, Clarke KV, Doan TT, Kulp JL. BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation. J Chem Inf Model 2023. [PMID: 37406353 DOI: 10.1021/acs.jcim.3c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
4
Derry A, Altman RB. COLLAPSE: A representation learning framework for identification and characterization of protein structural sites. Protein Sci 2023;32:e4541. [PMID: 36519247 PMCID: PMC9847082 DOI: 10.1002/pro.4541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
5
Yang L, He W, Yun Y, Gao Y, Zhu Z, Teng M, Liang Z, Niu L. Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022;20:765-779. [PMID: 35288344 PMCID: PMC9881048 DOI: 10.1016/j.gpb.2021.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 06/30/2021] [Accepted: 09/27/2021] [Indexed: 01/31/2023]
6
CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities. J Comput Aided Mol Des 2021;35:737-750. [PMID: 34050420 DOI: 10.1007/s10822-021-00390-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
7
Eguida M, Rognan D. A Computer Vision Approach to Align and Compare Protein Cavities: Application to Fragment-Based Drug Design. J Med Chem 2020;63:7127-7142. [DOI: 10.1021/acs.jmedchem.0c00422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
8
Torng W, Altman RB. High precision protein functional site detection using 3D convolutional neural networks. Bioinformatics 2020;35:1503-1512. [PMID: 31051039 PMCID: PMC6499237 DOI: 10.1093/bioinformatics/bty813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/14/2018] [Accepted: 09/19/2018] [Indexed: 12/02/2022]  Open
9
A deep learning framework to predict binding preference of RNA constituents on protein surface. Nat Commun 2019;10:4941. [PMID: 31666519 PMCID: PMC6821705 DOI: 10.1038/s41467-019-12920-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022]  Open
10
Marchand JR, Caflisch A. In silico fragment-based drug design with SEED. Eur J Med Chem 2018;156:907-917. [PMID: 30064119 DOI: 10.1016/j.ejmech.2018.07.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 12/13/2022]
11
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates. Structure 2018;26:565-571.e3. [PMID: 29551288 PMCID: PMC5890617 DOI: 10.1016/j.str.2018.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/26/2018] [Accepted: 02/09/2018] [Indexed: 11/22/2022]
12
Identification of Histamine H3 Receptor Ligands Using a New Crystal Structure Fragment-based Method. Sci Rep 2017;7:4829. [PMID: 28684785 PMCID: PMC5500575 DOI: 10.1038/s41598-017-05058-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/23/2017] [Indexed: 01/14/2023]  Open
13
Torng W, Altman RB. 3D deep convolutional neural networks for amino acid environment similarity analysis. BMC Bioinformatics 2017;18:302. [PMID: 28615003 PMCID: PMC5472009 DOI: 10.1186/s12859-017-1702-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/22/2017] [Indexed: 01/08/2023]  Open
14
He B, Lu C, Zheng G, He X, Wang M, Chen G, Zhang G, Lu A. Combination therapeutics in complex diseases. J Cell Mol Med 2016;20:2231-2240. [PMID: 27605177 PMCID: PMC5134672 DOI: 10.1111/jcmm.12930] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022]  Open
15
Grove LE, Vajda S, Kozakov D. Computational Methods to Support Fragment-based Drug Discovery. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
16
Chartier M, Adriansen E, Najmanovich R. IsoMIF Finder: online detection of binding site molecular interaction field similarities. Bioinformatics 2015;32:621-3. [PMID: 26504139 PMCID: PMC4743630 DOI: 10.1093/bioinformatics/btv616] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/17/2015] [Indexed: 11/25/2022]  Open
17
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
18
Successful generation of structural information for fragment-based drug discovery. Drug Discov Today 2015;20:1104-11. [DOI: 10.1016/j.drudis.2015.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/12/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
19
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]
20
Chartier M, Najmanovich R. Detection of Binding Site Molecular Interaction Field Similarities. J Chem Inf Model 2015;55:1600-15. [PMID: 26158641 DOI: 10.1021/acs.jcim.5b00333] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
21
Hussein HA, Borrel A, Geneix C, Petitjean M, Regad L, Camproux AC. PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins. Nucleic Acids Res 2015;43:W436-42. [PMID: 25956651 PMCID: PMC4489252 DOI: 10.1093/nar/gkv462] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/27/2015] [Indexed: 12/21/2022]  Open
22
Borrel A, Regad L, Xhaard H, Petitjean M, Camproux AC. PockDrug: A Model for Predicting Pocket Druggability That Overcomes Pocket Estimation Uncertainties. J Chem Inf Model 2015;55:882-95. [PMID: 25835082 DOI: 10.1021/ci5006004] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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