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For: Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. J Proteome Res 2021;20:1178-1189. [PMID: 33393786 PMCID: PMC7867644 DOI: 10.1021/acs.jproteome.0c00359] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Number Cited by Other Article(s)
1
Wuyun Q, Chen Y, Shen Y, Cao Y, Hu G, Cui W, Gao J, Zheng W. Recent Progress of Protein Tertiary Structure Prediction. Molecules 2024;29:832. [PMID: 38398585 PMCID: PMC10893003 DOI: 10.3390/molecules29040832] [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: 12/30/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024]  Open
2
Begum MN, Mahtarin R, Islam MT, Ahmed S, Konika TK, Mannoor K, Akhteruzzaman S, Qadri F. Molecular investigation of TSHR gene in Bangladeshi congenital hypothyroid patients. PLoS One 2023;18:e0282553. [PMID: 37561783 PMCID: PMC10414570 DOI: 10.1371/journal.pone.0282553] [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: 02/17/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023]  Open
3
Lee M. Recent Advances in Deep Learning for Protein-Protein Interaction Analysis: A Comprehensive Review. Molecules 2023;28:5169. [PMID: 37446831 DOI: 10.3390/molecules28135169] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]  Open
4
Guerler A, Baker D, van den Beek M, Gruening B, Bouvier D, Coraor N, Shank SD, Zehr JD, Schatz MC, Nekrutenko A. Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. BMC Bioinformatics 2023;24:263. [PMID: 37353753 PMCID: PMC10288729 DOI: 10.1186/s12859-023-05389-8] [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: 06/20/2022] [Accepted: 06/15/2023] [Indexed: 06/25/2023]  Open
5
Pelletier JF, Glass JI, Strychalski EA. Cellular mechanics during division of a genomically minimal cell. Trends Cell Biol 2022;32:900-907. [PMID: 35907702 DOI: 10.1016/j.tcb.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 01/21/2023]
6
Soleymani F, Paquet E, Viktor H, Michalowski W, Spinello D. Protein-protein interaction prediction with deep learning: A comprehensive review. Comput Struct Biotechnol J 2022;20:5316-5341. [PMID: 36212542 PMCID: PMC9520216 DOI: 10.1016/j.csbj.2022.08.070] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/15/2022]  Open
7
Bianchi D, Pelletier JF, Hutchison CA, Glass JI, Luthey-Schulten Z. Toward the Complete Functional Characterization of a Minimal Bacterial Proteome. J Phys Chem B 2022;126:6820-6834. [PMID: 36048731 PMCID: PMC9483919 DOI: 10.1021/acs.jpcb.2c04188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/10/2022] [Indexed: 11/29/2022]
8
LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022;4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]  Open
9
Kondratyeva L, Alekseenko I, Chernov I, Sverdlov E. Data Incompleteness May form a Hard-to-Overcome Barrier to Decoding Life's Mechanism. BIOLOGY 2022;11:1208. [PMID: 36009835 PMCID: PMC9404739 DOI: 10.3390/biology11081208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022]
10
I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction. Nat Protoc 2022;17:2326-2353. [PMID: 35931779 DOI: 10.1038/s41596-022-00728-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/24/2022] [Indexed: 01/17/2023]
11
Landon S, Chalkley O, Breese G, Grierson C, Marucci L. Understanding Metabolic Flux Behaviour in Whole-Cell Model Output. Front Mol Biosci 2021;8:732079. [PMID: 34977150 PMCID: PMC8718694 DOI: 10.3389/fmolb.2021.732079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022]  Open
12
Pedreira T, Elfmann C, Singh N, Stülke J. SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A. Protein Sci 2021;31:54-62. [PMID: 34515387 PMCID: PMC8740822 DOI: 10.1002/pro.4179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022]
13
Vafaee R, Tavirani MR, Tavirani SR, Razzaghi M. Assessment of cancer prevention effect of exercise. Hum Antibodies 2021;30:31-36. [PMID: 34459390 DOI: 10.3233/hab-210454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
14
Aljindan RY, Al-Subaie AM, Al-Ohali AI, Kumar D T, Doss C GP, Kamaraj B. Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Comput Biol Med 2021;135:104654. [PMID: 34346317 PMCID: PMC8282961 DOI: 10.1016/j.compbiomed.2021.104654] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
15
Pearce R, Zhang Y. Toward the solution of the protein structure prediction problem. J Biol Chem 2021;297:100870. [PMID: 34119522 PMCID: PMC8254035 DOI: 10.1016/j.jbc.2021.100870] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/20/2022]  Open
16
Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli. J Mol Biol 2021;433:166944. [PMID: 33741411 DOI: 10.1016/j.jmb.2021.166944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
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