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For: Zhao R, Cang Z, Tong Y, Wei GW. Protein pocket detection via convex hull surface evolution and associated Reeb graph. Bioinformatics 2019;34:i830-i837. [PMID: 30423105 DOI: 10.1093/bioinformatics/bty598] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
Number Cited by Other Article(s)
1
Zhang Y, Shen C, Xia K. Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction. Brief Bioinform 2024;25:bbae465. [PMID: 39323091 PMCID: PMC11424509 DOI: 10.1093/bib/bbae465] [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: 04/29/2024] [Revised: 08/07/2024] [Accepted: 09/05/2024] [Indexed: 09/27/2024]  Open
2
Karki R, Gadiya Y, Gribbon P, Zaliani A. Pharmacophore-Based Machine Learning Model To Predict Ligand Selectivity for E3 Ligase Binders. ACS OMEGA 2023;8:30177-30185. [PMID: 37636935 PMCID: PMC10448689 DOI: 10.1021/acsomega.3c02803] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023]
3
Wee J, Bianconi G, Xia K. Persistent Dirac for molecular representation. Sci Rep 2023;13:11183. [PMID: 37433870 DOI: 10.1038/s41598-023-37853-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023]  Open
4
Choo HY, Wee J, Shen C, Xia K. Fingerprint-Enhanced Graph Attention Network (FinGAT) Model for Antibiotic Discovery. J Chem Inf Model 2023;63:2928-2935. [PMID: 37167016 DOI: 10.1021/acs.jcim.3c00045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
5
Kumar S, Choudhary M. Structural and theoretical investigations, Hirshfeld surface analysis and anti-SARS CoV-2 of nickel (II) coordination complex. J Biomol Struct Dyn 2023;41:402-422. [PMID: 34842499 DOI: 10.1080/07391102.2021.2006089] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
6
Liu J, Xia KL, Wu J, Yau SST, Wei GW. Biomolecular Topology: Modelling and Analysis. ACTA MATHEMATICA SINICA, ENGLISH SERIES 2022;38:1901-1938. [PMID: 36407804 PMCID: PMC9640850 DOI: 10.1007/s10114-022-2326-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/12/2022] [Indexed: 05/25/2023]
7
Liu X, Feng H, Wu J, Xia K. Hom-Complex-Based Machine Learning (HCML) for the Prediction of Protein-Protein Binding Affinity Changes upon Mutation. J Chem Inf Model 2022;62:3961-3969. [PMID: 36040839 DOI: 10.1021/acs.jcim.2c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
8
Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022;122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
9
Schauperl M, Denny RA. AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges. J Chem Inf Model 2022;62:3142-3156. [PMID: 35727311 DOI: 10.1021/acs.jcim.2c00026] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
10
Lu Q. Identifying molecular structural features by pattern recognition methods. RSC Adv 2022;12:17559-17569. [PMID: 35765452 PMCID: PMC9192268 DOI: 10.1039/d2ra00764a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/06/2022] [Indexed: 11/21/2022]  Open
11
Alfarraj A, Wei GW. Geometric algebra generation of molecular surfaces. J R Soc Interface 2022;19:20220117. [PMID: 35414214 PMCID: PMC9006026 DOI: 10.1098/rsif.2022.0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
12
Liu X, Feng H, Wu J, Xia K. Dowker complex based machine learning (DCML) models for protein-ligand binding affinity prediction. PLoS Comput Biol 2022;18:e1009943. [PMID: 35385478 PMCID: PMC8985993 DOI: 10.1371/journal.pcbi.1009943] [Citation(s) in RCA: 12] [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: 09/14/2021] [Accepted: 02/21/2022] [Indexed: 11/19/2022]  Open
13
Wee J, Xia K. Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction. Brief Bioinform 2022;23:6533501. [PMID: 35189639 DOI: 10.1093/bib/bbac024] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022]  Open
14
Jiang P, Chi Y, Li XS, Liu X, Hua XS, Xia K. Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design. Brief Bioinform 2022;23:6485012. [PMID: 34958660 DOI: 10.1093/bib/bbab527] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/01/2021] [Accepted: 11/14/2021] [Indexed: 01/05/2023]  Open
15
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]
16
Aggarwal R, Gupta A, Chelur V, Jawahar CV, Priyakumar UD. DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks. J Chem Inf Model 2021;62:5069-5079. [PMID: 34374539 DOI: 10.1021/acs.jcim.1c00799] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
17
Wee J, Xia K. Forman persistent Ricci curvature (FPRC)-based machine learning models for protein-ligand binding affinity prediction. Brief Bioinform 2021;22:6262241. [PMID: 33940588 DOI: 10.1093/bib/bbab136] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/14/2021] [Accepted: 03/23/2021] [Indexed: 01/01/2023]  Open
18
Liu X, Feng H, Wu J, Xia K. Persistent spectral hypergraph based machine learning (PSH-ML) for protein-ligand binding affinity prediction. Brief Bioinform 2021;22:6219114. [PMID: 33837771 DOI: 10.1093/bib/bbab127] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022]  Open
19
Zhao R, Wang M, Chen J, Tong Y, Wei GW. The de Rham-Hodge Analysis and Modeling of Biomolecules. Bull Math Biol 2020;82:108. [PMID: 32770408 PMCID: PMC8137271 DOI: 10.1007/s11538-020-00783-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 07/20/2020] [Indexed: 12/18/2022]
20
Nguyen DD, Cang Z, Wei GW. A review of mathematical representations of biomolecular data. Phys Chem Chem Phys 2020;22:4343-4367. [PMID: 32067019 PMCID: PMC7081943 DOI: 10.1039/c9cp06554g] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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