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For: Fang J. A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. Brief Bioinform 2019;21:1285-1292. [PMID: 31273374 DOI: 10.1093/bib/bbz071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/14/2019] [Accepted: 05/16/2019] [Indexed: 01/02/2023]  Open
Number Cited by Other Article(s)
1
Dou Z, He J, Han C, Wu X, Wan L, Yang J, Zheng Y, Gong B, Wang L. qProtein: Exploring Physical Features of Protein Thermostability Based on Structural Proteomics. J Chem Inf Model 2024;64:7885-7894. [PMID: 39375829 DOI: 10.1021/acs.jcim.4c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
2
Han J, Ullah M, Andoh V, Khan MN, Feng Y, Guo Z, Chen H. Engineering Bacterial Chitinases for Industrial Application: From Protein Engineering to Bacterial Strains Mutation! A Comprehensive Review of Physical, Molecular, and Computational Approaches. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024;72:23082-23096. [PMID: 39388625 DOI: 10.1021/acs.jafc.4c06856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
3
Su Z, El Hage M, Linnebacher M. Mutation patterns in colorectal cancer and their relationship with prognosis. Heliyon 2024;10:e36550. [PMID: 39263143 PMCID: PMC11387246 DOI: 10.1016/j.heliyon.2024.e36550] [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: 05/28/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024]  Open
4
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
5
Bernett J, Blumenthal DB, Grimm DG, Haselbeck F, Joeres R, Kalinina OV, List M. Guiding questions to avoid data leakage in biological machine learning applications. Nat Methods 2024;21:1444-1453. [PMID: 39122953 DOI: 10.1038/s41592-024-02362-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/26/2024] [Indexed: 08/12/2024]
6
Cuturello F, Celoria M, Ansuini A, Cazzaniga A. Enhancing predictions of protein stability changes induced by single mutations using MSA-based Language Models. Bioinformatics 2024;40:btae447. [PMID: 39012369 PMCID: PMC11269464 DOI: 10.1093/bioinformatics/btae447] [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: 04/16/2024] [Revised: 06/19/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]  Open
7
Narayanan KK, Weigle AT, Xu L, Mi X, Zhang C, Chen LQ, Procko E, Shukla D. Deep mutational scanning reveals sequence to function constraints for SWEET family transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601307. [PMID: 39005363 PMCID: PMC11244857 DOI: 10.1101/2024.06.28.601307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
8
Sun X, Yang S, Wu Z, Su J, Hu F, Chang F, Li C. PMSPcnn: Predicting protein stability changes upon single point mutations with convolutional neural network. Structure 2024;32:838-848.e3. [PMID: 38508191 DOI: 10.1016/j.str.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/19/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
9
Qiu Y, Huang T, Cai YD. Review of predicting protein stability changes upon variations. Proteomics 2024;24:e2300371. [PMID: 38643379 DOI: 10.1002/pmic.202300371] [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: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/22/2024]
10
Zhang Y, Wu K, Li Y, Wu S, Warshel A, Bai C. Predicting Mutational Effects on Ca2+-Activated Chloride Conduction of TMEM16A Based on a Simulation Study. J Am Chem Soc 2024;146:4665-4679. [PMID: 38319142 DOI: 10.1021/jacs.3c11940] [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] [Indexed: 02/07/2024]
11
Cheon H, Kim JH, Kim JS, Park JB. Valorization of single-carbon chemicals by using carboligases as key enzymes. Curr Opin Biotechnol 2024;85:103047. [PMID: 38128199 DOI: 10.1016/j.copbio.2023.103047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
12
Zheng F, Liu Y, Yang Y, Wen Y, Li M. Assessing computational tools for predicting protein stability changes upon missense mutations using a new dataset. Protein Sci 2024;33:e4861. [PMID: 38084013 PMCID: PMC10751734 DOI: 10.1002/pro.4861] [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: 09/28/2023] [Revised: 11/14/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
13
Liu Z, Bao Y, Wang W, Pan L, Wang H, Lin GN. Emden: A novel method integrating graph and transformer representations for predicting the effect of mutations on clinical drug response. Comput Biol Med 2023;167:107678. [PMID: 37976823 DOI: 10.1016/j.compbiomed.2023.107678] [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: 10/22/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
14
Wang S, Tang H, Shan P, Wu Z, Zuo L. ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks. Comput Biol Chem 2023;107:107952. [PMID: 37643501 DOI: 10.1016/j.compbiolchem.2023.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
15
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]
16
Umerenkov D, Nikolaev F, Shashkova TI, Strashnov PV, Sindeeva M, Shevtsov A, Ivanisenko NV, Kardymon OL. PROSTATA: a framework for protein stability assessment using transformers. Bioinformatics 2023;39:btad671. [PMID: 37935419 PMCID: PMC10651431 DOI: 10.1093/bioinformatics/btad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]  Open
17
Dhiman A, Purohit R. Identification of potential mutational hotspots in serratiopeptidase to address its poor pH tolerance issue. J Biomol Struct Dyn 2023;41:8831-8843. [PMID: 36307910 DOI: 10.1080/07391102.2022.2137699] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/14/2022] [Indexed: 10/31/2022]
18
Zhang G, Luo Y, Dai X, Dai Z. Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities. Brief Bioinform 2023;24:bbad333. [PMID: 37775147 DOI: 10.1093/bib/bbad333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 10/01/2023]  Open
19
Sieg J, Rarey M. Searching similar local 3D micro-environments in protein structure databases with MicroMiner. Brief Bioinform 2023;24:bbad357. [PMID: 37833838 DOI: 10.1093/bib/bbad357] [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: 06/09/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]  Open
20
Wang J, Zhang H, Chen N, Zeng T, Ai X, Wu K. PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks. Animals (Basel) 2023;13:2935. [PMID: 37760334 PMCID: PMC10526013 DOI: 10.3390/ani13182935] [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: 07/20/2023] [Revised: 08/21/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]  Open
21
Liu Z, Qian W, Cai W, Song W, Wang W, Maharjan DT, Cheng W, Chen J, Wang H, Xu D, Lin GN. Inferring the Effects of Protein Variants on Protein-Protein Interactions with Interpretable Transformer Representations. RESEARCH (WASHINGTON, D.C.) 2023;6:0219. [PMID: 37701056 PMCID: PMC10494974 DOI: 10.34133/research.0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/20/2023] [Indexed: 09/14/2023]
22
Pandey P, Panday SK, Rimal P, Ancona N, Alexov E. Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations. Int J Mol Sci 2023;24:12073. [PMID: 37569449 PMCID: PMC10418460 DOI: 10.3390/ijms241512073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023]  Open
23
Blaabjerg LM, Kassem MM, Good LL, Jonsson N, Cagiada M, Johansson KE, Boomsma W, Stein A, Lindorff-Larsen K. Rapid protein stability prediction using deep learning representations. eLife 2023;12:e82593. [PMID: 37184062 PMCID: PMC10266766 DOI: 10.7554/elife.82593] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/12/2023] [Indexed: 05/16/2023]  Open
24
Dou Z, Sun Y, Jiang X, Wu X, Li Y, Gong B, Wang L. Data-driven strategies for the computational design of enzyme thermal stability: trends, perspectives, and prospects. Acta Biochim Biophys Sin (Shanghai) 2023;55:343-355. [PMID: 37143326 PMCID: PMC10160227 DOI: 10.3724/abbs.2023033] [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: 07/06/2022] [Accepted: 11/23/2022] [Indexed: 03/05/2023]  Open
25
Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel) 2023;15:1958. [PMID: 37046619 PMCID: PMC10093138 DOI: 10.3390/cancers15071958] [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: 10/27/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023]  Open
26
Pennica C, Hanna G, Islam SA, JE Sternberg M, David A. Missense3D-PPI: a web resource to predict the impact of missense variants at protein interfaces using 3D structural data. J Mol Biol 2023. [DOI: 10.1016/j.jmb.2023.168060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
27
Lihan M, Lupyan D, Oehme D. Target-template relationships in protein structure prediction and their effect on the accuracy of thermostability calculations. Protein Sci 2023;32:e4557. [PMID: 36573828 PMCID: PMC9878467 DOI: 10.1002/pro.4557] [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: 09/20/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
28
Alteration of Chain-Length Selectivity and Thermostability of Rhizopus oryzae Lipase via Virtual Saturation Mutagenesis Coupled with Disulfide Bond Design. Appl Environ Microbiol 2023;89:e0187822. [PMID: 36602359 PMCID: PMC9888275 DOI: 10.1128/aem.01878-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
29
Hu R, Fu L, Chen Y, Chen J, Qiao Y, Si T. Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments. Brief Bioinform 2023;24:6958505. [PMID: 36562723 DOI: 10.1093/bib/bbac570] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]  Open
30
Chandra A, Tünnermann L, Löfstedt T, Gratz R. Transformer-based deep learning for predicting protein properties in the life sciences. eLife 2023;12:e82819. [PMID: 36651724 PMCID: PMC9848389 DOI: 10.7554/elife.82819] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023]  Open
31
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] [Abstract] [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
32
Muacevic A, Adler JR. Comparison of In Vitro and In Silico Assessments of Human Galactose-1-Phosphate Uridylyltransferase Coding Variants. Cureus 2023;15:e33592. [PMID: 36788839 PMCID: PMC9910814 DOI: 10.7759/cureus.33592] [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: 10/17/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023]  Open
33
Wang S, Tang H, Zhao Y, Zuo L. BayeStab: Predicting effects of mutations on protein stability with uncertainty quantification. Protein Sci 2022;31:e4467. [PMID: 36217239 PMCID: PMC9601791 DOI: 10.1002/pro.4467] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/11/2022]
34
Velecký J, Hamsikova M, Stourac J, Musil M, Damborsk J, Bednar D, Mazurenko S. SoluProtMutDB: a manually curated database of protein solubility changes upon mutations. Comput Struct Biotechnol J 2022;20:6339-6347. [DOI: 10.1016/j.csbj.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]  Open
35
Oliveira MLG, Castelli EC, Veiga‐Castelli LC, Pereira ALE, Marcorin L, Carratto TMT, Souza AS, Andrade HS, Simões AL, Donadi EA, Courtin D, Sabbagh A, Giuliatti S, Mendes‐Junior CT. Genetic diversity of the LILRB1 and LILRB2 coding regions in an admixed Brazilian population sample. HLA 2022;100:325-348. [DOI: 10.1111/tan.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
36
Gao Q, Deng H, Yang Z, Yang Q, Zhang Y, Yuan X, Zeng M, Guo M, Zeng W, Jiang X, Yu B. Sodium danshensu attenuates cerebral ischemia–reperfusion injury by targeting AKT1. Front Pharmacol 2022;13:946668. [PMID: 36188542 PMCID: PMC9520076 DOI: 10.3389/fphar.2022.946668] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/22/2022] [Indexed: 12/02/2022]  Open
37
Iqbal S, Ge F, Li F, Akutsu T, Zheng Y, Gasser RB, Yu DJ, Webb GI, Song J. PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. J Chem Inf Model 2022;62:4270-4282. [PMID: 35973091 DOI: 10.1021/acs.jcim.2c00799] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
38
Casadio R, Savojardo C, Fariselli P, Capriotti E, Martelli PL. Turning Failures into Applications: The Problem of Protein ΔΔG Prediction. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022;2449:169-185. [PMID: 35507262 DOI: 10.1007/978-1-0716-2095-3_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
39
Montanucci L, Capriotti E, Birolo G, Benevenuta S, Pancotti C, Lal D, Fariselli P. DDGun: an untrained predictor of protein stability changes upon amino acid variants. Nucleic Acids Res 2022;50:W222-W227. [PMID: 35524565 PMCID: PMC9252764 DOI: 10.1093/nar/gkac325] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/15/2022] [Accepted: 05/04/2022] [Indexed: 01/22/2023]  Open
40
Kebabci N, Timucin AC, Timucin E. Toward Compilation of Balanced Protein Stability Data Sets: Flattening the ΔΔG Curve through Systematic Enrichment. J Chem Inf Model 2022;62:1345-1355. [PMID: 35201762 DOI: 10.1021/acs.jcim.2c00054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
41
Baek KT, Kepp KP. Data set and fitting dependencies when estimating protein mutant stability: Toward simple, balanced, and interpretable models. J Comput Chem 2022;43:504-518. [PMID: 35040492 DOI: 10.1002/jcc.26810] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 12/27/2022]
42
Pancotti C, Benevenuta S, Birolo G, Alberini V, Repetto V, Sanavia T, Capriotti E, Fariselli P. Predicting protein stability changes upon single-point mutation: a thorough comparison of the available tools on a new dataset. Brief Bioinform 2022;23:6502552. [PMID: 35021190 PMCID: PMC8921618 DOI: 10.1093/bib/bbab555] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 12/13/2022]  Open
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Artificial intelligence challenges for predicting the impact of mutations on protein stability. Curr Opin Struct Biol 2021;72:161-168. [PMID: 34922207 DOI: 10.1016/j.sbi.2021.11.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/15/2021] [Accepted: 11/08/2021] [Indexed: 01/17/2023]
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Narykov O, Johnson NT, Korkin D. Predicting protein interaction network perturbation by alternative splicing with semi-supervised learning. Cell Rep 2021;37:110045. [PMID: 34818539 DOI: 10.1016/j.celrep.2021.110045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/21/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]  Open
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Rostami N, Choupani E, Hernandez Y, Arab SS, Jazayeri SM, Gomari MM. SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. J Cell Biochem 2021;123:417-430. [PMID: 34783057 PMCID: PMC8657535 DOI: 10.1002/jcb.30181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/20/2022]
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Rogers AW, Vega-Ramon F, Yan J, Del Río-Chanona EA, Jing K, Zhang D. A transfer learning approach for predictive modeling of bioprocesses using small data. Biotechnol Bioeng 2021;119:411-422. [PMID: 34716712 DOI: 10.1002/bit.27980] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/28/2021] [Indexed: 11/06/2022]
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Samaga YBL, Raghunathan S, Priyakumar UD. SCONES: Self-Consistent Neural Network for Protein Stability Prediction Upon Mutation. J Phys Chem B 2021;125:10657-10671. [PMID: 34546056 DOI: 10.1021/acs.jpcb.1c04913] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Marabotti A, Del Prete E, Scafuri B, Facchiano A. Performance of Web tools for predicting changes in protein stability caused by mutations. BMC Bioinformatics 2021;22:345. [PMID: 34225665 PMCID: PMC8256537 DOI: 10.1186/s12859-021-04238-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/18/2021] [Indexed: 01/17/2023]  Open
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021;54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
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Scherer M, Fleishman SJ, Jones PR, Dandekar T, Bencurova E. Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals. Front Bioeng Biotechnol 2021;9:673005. [PMID: 34211966 PMCID: PMC8239229 DOI: 10.3389/fbioe.2021.673005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022]  Open
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