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For: Wu F, Jin S, Jiang Y, Jin X, Tang B, Niu Z, Liu X, Zhang Q, Zeng X, Li SZ. Pre-Training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding. Adv Sci (Weinh) 2022;9:e2203796. [PMID: 36202759 PMCID: PMC9685463 DOI: 10.1002/advs.202203796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/07/2022] [Indexed: 05/16/2023]
Number Cited by Other Article(s)
1
Thaingtamtanha T, Ravichandran R, Gentile F. On the application of artificial intelligence in virtual screening. Expert Opin Drug Discov 2025:1-13. [PMID: 40388244 DOI: 10.1080/17460441.2025.2508866] [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: 02/17/2025] [Revised: 04/22/2025] [Accepted: 05/16/2025] [Indexed: 05/21/2025]
2
Li J, Gong X. Harnessing pre-trained models for accurate prediction of protein-ligand binding affinity. BMC Bioinformatics 2025;26:55. [PMID: 39962390 PMCID: PMC11834573 DOI: 10.1186/s12859-025-06064-w] [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: 11/03/2024] [Accepted: 01/22/2025] [Indexed: 02/20/2025]  Open
3
Hu Y, Yang H, Li M, Zhong Z, Zhou Y, Bai F, Wang Q. Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2400884. [PMID: 39387316 PMCID: PMC11600214 DOI: 10.1002/advs.202400884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 07/22/2024] [Indexed: 10/15/2024]
4
Min Y, Wei Y, Wang P, Wang X, Li H, Wu N, Bauer S, Zheng S, Shi Y, Wang Y, Wu J, Zhao D, Zeng J. From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2405404. [PMID: 39206846 PMCID: PMC11516055 DOI: 10.1002/advs.202405404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/29/2024] [Indexed: 09/04/2024]
5
Wang H, Chen B, Sun H, Zhang Y. Carbon-based molecular properties efficiently predicted by deep learning-based quantum chemical simulation with large language models. Comput Biol Med 2024;176:108531. [PMID: 38728991 DOI: 10.1016/j.compbiomed.2024.108531] [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: 02/11/2024] [Revised: 04/21/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
6
Visani GM, Pun MN, Angaji A, Nourmohammad A. Holographic-(V)AE: An end-to-end SO(3)-equivariant (variational) autoencoder in Fourier space. PHYSICAL REVIEW RESEARCH 2024;6:023006. [PMID: 39711614 PMCID: PMC11661850 DOI: 10.1103/physrevresearch.6.023006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
7
Wang H. Prediction of protein-ligand binding affinity via deep learning models. Brief Bioinform 2024;25:bbae081. [PMID: 38446737 PMCID: PMC10939342 DOI: 10.1093/bib/bbae081] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/31/2024] [Indexed: 03/08/2024]  Open
8
Gu S, Liu H, Liu L, Hou T, Kang Y. Artificial intelligence methods in kinase target profiling: Advances and challenges. Drug Discov Today 2023;28:103796. [PMID: 37805065 DOI: 10.1016/j.drudis.2023.103796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
9
Yue Y, Li S, Wang L, Liu H, Tong HHY, He S. MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions. Brief Bioinform 2023;24:bbad310. [PMID: 37651610 PMCID: PMC10516393 DOI: 10.1093/bib/bbad310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/12/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023]  Open
10
Wu F, Courty N, Jin S, Li SZ. Improving molecular representation learning with metric learning-enhanced optimal transport. PATTERNS (NEW YORK, N.Y.) 2023;4:100714. [PMID: 37123438 PMCID: PMC10140620 DOI: 10.1016/j.patter.2023.100714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/29/2022] [Accepted: 03/01/2023] [Indexed: 05/02/2023]
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