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For: Pak MA, Ivankov DN. Best templates outperform homology models in predicting the impact of mutations on protein stability. Bioinformatics 2022;38:4312-4320. [PMID: 35894930 DOI: 10.1093/bioinformatics/btac515] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 05/31/2022] [Indexed: 12/24/2022]  Open
Number Cited by Other Article(s)
1
Makwana SH, Sharma T, Mahapatra MK, Kumari M, Jain A, Shrivastava SK, Mandal CC. Targeting TRIM26: Unveiling an Oncogene and Identification of Plant Metabolites as a Potential Therapeutics for Breast Cancer. J Cell Biochem 2024;125:e30644. [PMID: 39286999 DOI: 10.1002/jcb.30644] [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: 04/15/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024]
2
Hussin A, Nathan S, Shahidan MA, Nor Rahim MY, Zainun MY, Khairuddin NAN, Ibrahim N. Identification and mechanism determination of the efflux pump subunit amrB gene mutations linked to gentamicin susceptibility in clinical Burkholderia pseudomallei from Malaysian Borneo. Mol Genet Genomics 2024;299:12. [PMID: 38381232 DOI: 10.1007/s00438-024-02105-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: 07/18/2023] [Accepted: 12/29/2023] [Indexed: 02/22/2024]
3
Melnik TN, Majorina MA, Vorobeva DE, Nagibina GS, Veselova VR, Glukhova KA, Pak MA, Ivankov DN, Uversky VN, Melnik BS. Design of stable circular permutants of the GroEL chaperone apical domain. Cell Commun Signal 2024;22:90. [PMID: 38303060 PMCID: PMC10836027 DOI: 10.1186/s12964-023-01426-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024]  Open
4
Malhotra N, Khatri S, Kumar A, Arun A, Daripa P, Fatihi S, Venkadesan S, Jain N, Thukral L. AI-based AlphaFold2 significantly expands the structural space of the autophagy pathway. Autophagy 2023;19:3201-3220. [PMID: 37516933 PMCID: PMC10621275 DOI: 10.1080/15548627.2023.2238578] [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: 06/07/2022] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]  Open
5
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
6
Lubin JH, Markosian C, Balamurugan D, Ma MT, Chen CH, Liu D, Pasqualini R, Arap W, Burley SK, Khare SD. Modeling of ACE2 and antibodies bound to SARS-CoV-2 provides insights into infectivity and immune evasion. JCI Insight 2023;8:e168296. [PMID: 37261904 PMCID: PMC10371346 DOI: 10.1172/jci.insight.168296] [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: 12/23/2022] [Accepted: 05/26/2023] [Indexed: 06/03/2023]  Open
7
Gerasimavicius L, Livesey BJ, Marsh JA. Correspondence between functional scores from deep mutational scans and predicted effects on protein stability. Protein Sci 2023;32:e4688. [PMID: 37243972 PMCID: PMC10273344 DOI: 10.1002/pro.4688] [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: 02/03/2023] [Revised: 04/19/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
8
Çiftci N, Akıncı A, Akbulut E, Çamtosun E, Dündar İ, Doğan M, Kayaş L. Clinical Characteristics and Genetic Analyses of Patients with Idiopathic Hypogonadotropic Hypogonadism. J Clin Res Pediatr Endocrinol 2023;15:160-171. [PMID: 36700485 PMCID: PMC10234052 DOI: 10.4274/jcrpe.galenos.2023.2022-10-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/16/2023] [Indexed: 01/27/2023]  Open
9
Yang P, Wang X, Ye J, Rao S, Zhou J, Du G, Liu S. Enhanced Thermostability and Catalytic Activity of Streptomyces mobaraenesis Transglutaminase by Rationally Engineering Its Flexible Regions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023;71:6366-6375. [PMID: 37039372 DOI: 10.1021/acs.jafc.3c00260] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
10
Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova ES, Kondrashov FA, Ivankov DN. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS One 2023;18:e0282689. [PMID: 36928239 PMCID: PMC10019719 DOI: 10.1371/journal.pone.0282689] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/21/2023] [Indexed: 03/17/2023]  Open
11
Valanciute A, Nygaard L, Zschach H, Maglegaard Jepsen M, Lindorff-Larsen K, Stein A. Accurate protein stability predictions from homology models. Comput Struct Biotechnol J 2022;21:66-73. [PMID: 36514339 PMCID: PMC9729920 DOI: 10.1016/j.csbj.2022.11.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]  Open
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