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For: Hernández IM, Dehouck Y, Bastolla U, López-Blanco JR, Chacón P. Predicting protein stability changes upon mutation using a simple orientational potential. Bioinformatics 2023;39:6984713. [PMID: 36629451 PMCID: PMC9850275 DOI: 10.1093/bioinformatics/btad011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/17/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023]  Open
Number Cited by Other Article(s)
1
Xu Y, Liu D, Gong H. Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy. NATURE COMPUTATIONAL SCIENCE 2024:10.1038/s43588-024-00716-2. [PMID: 39455825 DOI: 10.1038/s43588-024-00716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/03/2024] [Indexed: 10/28/2024]
2
Li D, Zhu Y, Zhang W, Liu J, Yang X, Liu Z, Wei D. AI Prediction of Structural Stability of Nanoproteins Based on Structures and Residue Properties by Mean Pooled Dual Graph Convolutional Network. Interdiscip Sci 2024:10.1007/s12539-024-00662-7. [PMID: 39367992 DOI: 10.1007/s12539-024-00662-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 09/18/2024] [Accepted: 09/22/2024] [Indexed: 10/07/2024]
3
Li SS, Liu ZM, Li J, Ma YB, Dong ZY, Hou JW, Shen FJ, Wang WB, Li QM, Su JG. Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method. BMC Bioinformatics 2024;25:282. [PMID: 39198740 PMCID: PMC11360314 DOI: 10.1186/s12859-024-05876-6] [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: 02/27/2024] [Accepted: 07/19/2024] [Indexed: 09/01/2024]  Open
4
Chen Y, Xu Y, Liu D, Xing Y, Gong H. An end-to-end framework for the prediction of protein structure and fitness from single sequence. Nat Commun 2024;15:7400. [PMID: 39191788 DOI: 10.1038/s41467-024-51776-x] [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: 02/27/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]  Open
5
Rollo C, Pancotti C, Birolo G, Rossi I, Sanavia T, Fariselli P. Influence of Model Structures on Predictors of Protein Stability Changes from Single-Point Mutations. Genes (Basel) 2023;14:2228. [PMID: 38137050 PMCID: PMC10742815 DOI: 10.3390/genes14122228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]  Open
6
Kouba P, Kohout P, Haddadi F, Bushuiev A, Samusevich R, Sedlar J, Damborsky J, Pluskal T, Sivic J, Mazurenko S. Machine Learning-Guided Protein Engineering. ACS Catal 2023;13:13863-13895. [PMID: 37942269 PMCID: PMC10629210 DOI: 10.1021/acscatal.3c02743] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/20/2023] [Indexed: 11/10/2023]
7
Gong H, Zhang Y, Dong C, Wang Y, Chen G, Liang B, Li H, Liu L, Xu J, Li G. Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction. Bioinformatics 2023;39:btad589. [PMID: 37740312 PMCID: PMC10918760 DOI: 10.1093/bioinformatics/btad589] [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: 04/25/2023] [Revised: 08/04/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023]  Open
8
Quan N, Eguchi Y, Geiler-Samerotte K. Intra-FCY1: a novel system to identify mutations that cause protein misfolding. Front Genet 2023;14:1198203. [PMID: 37745845 PMCID: PMC10512024 DOI: 10.3389/fgene.2023.1198203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023]  Open
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