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For: Marchi J, Galpern EA, Espada R, Ferreiro DU, Walczak AM, Mora T. Size and structure of the sequence space of repeat proteins. PLoS Comput Biol 2019;15:e1007282. [PMID: 31415557 PMCID: PMC6733475 DOI: 10.1371/journal.pcbi.1007282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 09/09/2019] [Accepted: 07/24/2019] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Bravi B, Di Gioacchino A, Fernandez-de-Cossio-Diaz J, Walczak AM, Mora T, Cocco S, Monasson R. A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity. eLife 2023;12:e85126. [PMID: 37681658 PMCID: PMC10522340 DOI: 10.7554/elife.85126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/07/2023] [Indexed: 09/09/2023]  Open
2
Sánchez IE, Galpern EA, Garibaldi MM, Ferreiro DU. Molecular Information Theory Meets Protein Folding. J Phys Chem B 2022;126:8655-8668. [PMID: 36282961 DOI: 10.1021/acs.jpcb.2c04532] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
3
Bitard-Feildel T. Navigating the amino acid sequence space between functional proteins using a deep learning framework. PeerJ Comput Sci 2021;7:e684. [PMID: 34616884 PMCID: PMC8459775 DOI: 10.7717/peerj-cs.684] [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: 03/25/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
4
Michael E, Simonson T. How much can physics do for protein design? Curr Opin Struct Biol 2021;72:46-54. [PMID: 34461593 DOI: 10.1016/j.sbi.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/03/2023]
5
Izert MA, Szybowska PE, Górna MW, Merski M. The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins. FRONTIERS IN BIOINFORMATICS 2021;1:696368. [PMID: 36303725 PMCID: PMC9581033 DOI: 10.3389/fbinf.2021.696368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/22/2021] [Indexed: 11/20/2022]  Open
6
Tian P, Best RB. Exploring the sequence fitness landscape of a bridge between protein folds. PLoS Comput Biol 2020;16:e1008285. [PMID: 33048928 PMCID: PMC7553338 DOI: 10.1371/journal.pcbi.1008285] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022]  Open
7
Galpern EA, Freiberger MI, Ferreiro DU. Large Ankyrin repeat proteins are formed with similar and energetically favorable units. PLoS One 2020;15:e0233865. [PMID: 32579546 PMCID: PMC7314423 DOI: 10.1371/journal.pone.0233865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/13/2020] [Indexed: 11/19/2022]  Open
8
Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes. Genetics 2020;214:1047-1057. [PMID: 32107278 DOI: 10.1534/genetics.120.302815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/18/2020] [Indexed: 11/18/2022]  Open
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