• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4832674)   Today's Articles (5691)
For: Sharir-Ivry A, Xia Y. Nature of Long-Range Evolutionary Constraint in Enzymes: Insights from Comparison to Pseudoenzymes with Similar Structures. Mol Biol Evol 2019;35:2597-2606. [PMID: 30202983 DOI: 10.1093/molbev/msy177] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Li Z, Chen M, Tian W, Wang L, Wu X. Investigating the role of polar amino acids driven by evolution in the active site architecture of GH11 xylanase. Int J Biol Macromol 2025;315:144464. [PMID: 40403789 DOI: 10.1016/j.ijbiomac.2025.144464] [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: 03/19/2025] [Revised: 05/09/2025] [Accepted: 05/19/2025] [Indexed: 05/24/2025]
2
Almeida de Jesus D, Batista DM, Monteiro EF, Salzman S, Carvalho LM, Santana K, André T. Structural changes and adaptative evolutionary constraints in FLOWERING LOCUS T and TERMINAL FLOWER1-like genes of flowering plants. Front Genet 2022;13:954015. [PMID: 36246591 PMCID: PMC9556947 DOI: 10.3389/fgene.2022.954015] [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: 05/26/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022]  Open
3
Learning the local landscape of protein structures with convolutional neural networks. J Biol Phys 2021;47:435-454. [PMID: 34751854 DOI: 10.1007/s10867-021-09593-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]  Open
4
Paul A, Subhadarshini S, Srinivasan N. Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles. Proteins 2021;90:747-764. [PMID: 34708889 DOI: 10.1002/prot.26271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/27/2023]
5
Echave J. Evolutionary coupling range varies widely among enzymes depending on selection pressure. Biophys J 2021;120:4320-4324. [PMID: 34480927 DOI: 10.1016/j.bpj.2021.08.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/19/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]  Open
6
Sharir-Ivry A, Xia Y. Quantifying evolutionary importance of protein sites: A Tale of two measures. PLoS Genet 2021;17:e1009476. [PMID: 33826605 PMCID: PMC8026052 DOI: 10.1371/journal.pgen.1009476] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022]  Open
7
The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences. BIOPHYSICA 2021. [DOI: 10.3390/biophysica1020008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
8
Paul A, Srinivasan N. Genome-wide and structural analyses of pseudokinases encoded in the genome of Arabidopsis thaliana provide functional insights. Proteins 2020;88:1620-1638. [PMID: 32667690 DOI: 10.1002/prot.25981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/26/2020] [Accepted: 07/12/2020] [Indexed: 12/31/2022]
9
A beginner's guide to molecular dynamics simulations and the identification of cross-correlation networks for enzyme engineering. Methods Enzymol 2020;643:15-49. [PMID: 32896280 DOI: 10.1016/bs.mie.2020.04.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
10
Sharir-Ivry A, Xia Y. Non-catalytic Binding Sites Induce Weaker Long-Range Evolutionary Rate Gradients than Catalytic Sites in Enzymes. J Mol Biol 2019;431:3860-3870. [DOI: 10.1016/j.jmb.2019.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/26/2019] [Accepted: 07/11/2019] [Indexed: 01/02/2023]
11
Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA. Emerging concepts in pseudoenzyme classification, evolution, and signaling. Sci Signal 2019;12:eaat9797. [PMID: 31409758 DOI: 10.1126/scisignal.aat9797] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
12
Sharir-Ivry A, Xia Y. Using Pseudoenzymes to Probe Evolutionary Design Principles of Enzymes. Evol Bioinform Online 2019;15:1176934319855937. [PMID: 31236007 PMCID: PMC6572901 DOI: 10.1177/1176934319855937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/15/2019] [Indexed: 12/24/2022]  Open
PrevPage 1 of 1 1Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA