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For: Ichinomiya T, Obayashi I, Hiraoka Y. Protein-Folding Analysis Using Features Obtained by Persistent Homology. Biophys J 2020;118:2926-2937. [PMID: 32428439 PMCID: PMC7300307 DOI: 10.1016/j.bpj.2020.04.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/16/2020] [Accepted: 04/17/2020] [Indexed: 10/25/2022]  Open
Number Cited by Other Article(s)
1
Amado D, Chaves OA, Cruz PF, Loureiro RJS, Almeida ZL, Jesus CSH, Serpa C, Brito RMM. Folding Kinetics and Volume Variation of the β-Hairpin Peptide Chignolin upon Ultrafast pH-Jumps. J Phys Chem B 2024;128:4898-4910. [PMID: 38733339 DOI: 10.1021/acs.jpcb.3c08271] [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: 05/13/2024]
2
Bou Dagher L, Madern D, Malbos P, Brochier-Armanet C. Persistent homology reveals strong phylogenetic signal in 3D protein structures. PNAS NEXUS 2024;3:pgae158. [PMID: 38689707 PMCID: PMC11058471 DOI: 10.1093/pnasnexus/pgae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
3
Ehiro T. Descriptor generation from Morgan fingerprint using persistent homology. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024;35:31-51. [PMID: 38234251 DOI: 10.1080/1062936x.2023.2301327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
4
Tarín-Pelló A, Suay-García B, Forés-Martos J, Falcó A, Pérez-Gracia MT. Computer-aided drug repurposing to tackle antibiotic resistance based on topological data analysis. Comput Biol Med 2023;166:107496. [PMID: 37793206 DOI: 10.1016/j.compbiomed.2023.107496] [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: 04/23/2023] [Revised: 08/29/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023]
5
Bobrowski O, Skraba P. A universal null-distribution for topological data analysis. Sci Rep 2023;13:12274. [PMID: 37507400 PMCID: PMC10382541 DOI: 10.1038/s41598-023-37842-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/28/2023] [Indexed: 07/30/2023]  Open
6
Skaf Y, Laubenbacher R. Topological data analysis in biomedicine: A review. J Biomed Inform 2022;130:104082. [PMID: 35508272 DOI: 10.1016/j.jbi.2022.104082] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/20/2022] [Accepted: 04/23/2022] [Indexed: 01/22/2023]
7
Le MQ, Taylor D. Persistent homology of convection cycles in network flows. Phys Rev E 2022;105:044311. [PMID: 35590622 DOI: 10.1103/physreve.105.044311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
8
Ichinomiya T. Topological data analysis gives two folding paths in HP35(nle-nle), double mutant of villin headpiece subdomain. Sci Rep 2022;12:2719. [PMID: 35177744 PMCID: PMC8854739 DOI: 10.1038/s41598-022-06682-x] [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: 05/11/2021] [Accepted: 02/04/2022] [Indexed: 11/16/2022]  Open
9
Moroni D, Pascali MA. Learning Topology: Bridging Computational Topology and Machine Learning. PATTERN RECOGNITION AND IMAGE ANALYSIS 2021. [DOI: 10.1134/s1054661821030184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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