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For: Kamiński K, Ludwiczak J, Jasiński M, Bukala A, Madaj R, Szczepaniak K, Dunin-Horkawicz S. Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. Brief Bioinform 2021;23:6375059. [PMID: 34571541 PMCID: PMC8769691 DOI: 10.1093/bib/bbab371] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/04/2021] [Accepted: 08/22/2021] [Indexed: 11/15/2022]  Open
Number Cited by Other Article(s)
1
Filgueiras JPC, Zámocký M, Turchetto-Zolet AC. Unraveling the evolutionary origin of the P5CS gene: a story of gene fusion and horizontal transfer. Front Mol Biosci 2024;11:1341684. [PMID: 38693917 PMCID: PMC11061531 DOI: 10.3389/fmolb.2024.1341684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]  Open
2
Vadaddi SM, Zhao Q, Savoie BM. Graph to Activation Energy Models Easily Reach Irreducible Errors but Show Limited Transferability. J Phys Chem A 2024;128:2543-2555. [PMID: 38517281 DOI: 10.1021/acs.jpca.3c07240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
3
Wang Z, Wang S, Li Y, Guo J, Wei Y, Mu Y, Zheng L, Li W. A new paradigm for applying deep learning to protein-ligand interaction prediction. Brief Bioinform 2024;25:bbae145. [PMID: 38581420 PMCID: PMC10998640 DOI: 10.1093/bib/bbae145] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]  Open
4
Han S, Lee JE, Kang S, So M, Jin H, Lee JH, Baek S, Jun H, Kim TY, Lee YS. Standigm ASK™: knowledge graph and artificial intelligence platform applied to target discovery in idiopathic pulmonary fibrosis. Brief Bioinform 2024;25:bbae035. [PMID: 38349059 PMCID: PMC10862655 DOI: 10.1093/bib/bbae035] [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: 11/07/2023] [Revised: 12/28/2023] [Indexed: 02/15/2024]  Open
5
Lin X, Chen J, Ma W, Tang W, Wang Y. EEG emotion recognition using improved graph neural network with channel selection. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023;231:107380. [PMID: 36745954 DOI: 10.1016/j.cmpb.2023.107380] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/11/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
6
Li G, Buric F, Zrimec J, Viknander S, Nielsen J, Zelezniak A, Engqvist MKM. Learning deep representations of enzyme thermal adaptation. Protein Sci 2022;31:e4480. [PMID: 36261883 PMCID: PMC9679980 DOI: 10.1002/pro.4480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/02/2022] [Accepted: 10/15/2022] [Indexed: 12/14/2022]
7
Ludwiczak J, Winski A, Dunin-Horkawicz S. Localpdb- a Python package to manage protein structures and their annotations. Bioinformatics 2022;38:2633-2635. [PMID: 35199148 PMCID: PMC9048648 DOI: 10.1093/bioinformatics/btac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/07/2022] [Accepted: 02/21/2022] [Indexed: 12/02/2022]  Open
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