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For: Das S, Lee D, Sillitoe I, Dawson NL, Lees JG, Orengo CA. Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. Bioinformatics 2015;31:3460-7. [PMID: 26139634 PMCID: PMC4612221 DOI: 10.1093/bioinformatics/btv398] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 06/24/2015] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
51
Zhang F, Song H, Zeng M, Li Y, Kurgan L, Li M. DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions. Proteomics 2019;19:e1900019. [PMID: 30941889 DOI: 10.1002/pmic.201900019] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/18/2019] [Indexed: 01/06/2023]
52
Distinct mechanisms of substrate selectivity in the DRE-TIM metallolyase superfamily: A role for the LeuA dimer regulatory domain. Arch Biochem Biophys 2019;664:1-8. [DOI: 10.1016/j.abb.2019.01.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/20/2022]
53
Ashford P, Pang CSM, Moya-García AA, Adeyelu T, Orengo CA. A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations. Sci Rep 2019;9:263. [PMID: 30670742 PMCID: PMC6343001 DOI: 10.1038/s41598-018-36401-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/13/2018] [Indexed: 12/31/2022]  Open
54
Sillitoe I, Dawson N, Lewis TE, Das S, Lees JG, Ashford P, Tolulope A, Scholes HM, Senatorov I, Bujan A, Ceballos Rodriguez-Conde F, Dowling B, Thornton J, Orengo CA. CATH: expanding the horizons of structure-based functional annotations for genome sequences. Nucleic Acids Res 2019;47:D280-D284. [PMID: 30398663 PMCID: PMC6323983 DOI: 10.1093/nar/gky1097] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/16/2018] [Accepted: 11/02/2018] [Indexed: 01/20/2023]  Open
55
Kulmanov M, Khan MA, Hoehndorf R, Wren J. DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinformatics 2018;34:660-668. [PMID: 29028931 PMCID: PMC5860606 DOI: 10.1093/bioinformatics/btx624] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/27/2017] [Indexed: 12/29/2022]  Open
56
Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells. Biochem J 2018;475:1909-1937. [PMID: 29626155 PMCID: PMC5989533 DOI: 10.1042/bcj20180043] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 02/07/2023]
57
Pagnuco IA, Revuelta MV, Bondino HG, Brun M, ten Have A. HMMER Cut-off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut-off threshold. PLoS One 2018;13:e0193757. [PMID: 29579071 PMCID: PMC5868777 DOI: 10.1371/journal.pone.0193757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 02/04/2018] [Indexed: 11/19/2022]  Open
58
You R, Zhang Z, Xiong Y, Sun F, Mamitsuka H, Zhu S. GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. Bioinformatics 2018. [DOI: 10.1093/bioinformatics/bty130] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
59
The Classification of Protein Domains. Methods Mol Biol 2018;1525:137-164. [PMID: 27896721 DOI: 10.1007/978-1-4939-6622-6_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
60
Rifaioglu AS, Doğan T, Saraç ÖS, Ersahin T, Saidi R, Atalay MV, Martin MJ, Cetin-Atalay R. Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants. Proteins 2017;86:135-151. [PMID: 29098713 DOI: 10.1002/prot.25416] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 10/24/2017] [Accepted: 11/01/2017] [Indexed: 12/24/2022]
61
Frappier V, Duran M, Keating AE. PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode. Protein Sci 2017;27:276-285. [PMID: 29024246 DOI: 10.1002/pro.3320] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 11/08/2022]
62
Mitchell JB. Enzyme function and its evolution. Curr Opin Struct Biol 2017;47:151-156. [PMID: 29107208 DOI: 10.1016/j.sbi.2017.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/29/2017] [Accepted: 10/02/2017] [Indexed: 01/10/2023]
63
Northey TC, Barešić A, Martin ACR. IntPred: a structure-based predictor of protein-protein interaction sites. Bioinformatics 2017;34:223-229. [PMID: 28968673 PMCID: PMC5860208 DOI: 10.1093/bioinformatics/btx585] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 08/21/2017] [Accepted: 09/15/2017] [Indexed: 11/17/2022]  Open
64
Moya-García A, Adeyelu T, Kruger FA, Dawson NL, Lees JG, Overington JP, Orengo C, Ranea JAG. Structural and Functional View of Polypharmacology. Sci Rep 2017;7:10102. [PMID: 28860623 PMCID: PMC5579063 DOI: 10.1038/s41598-017-10012-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023]  Open
65
Lam SD, Das S, Sillitoe I, Orengo C. An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences. Acta Crystallogr D Struct Biol 2017;73:628-640. [PMID: 28777078 PMCID: PMC5571743 DOI: 10.1107/s2059798317008920] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/14/2017] [Indexed: 12/02/2022]  Open
66
CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences. Methods Mol Biol 2017;1558:79-110. [PMID: 28150234 DOI: 10.1007/978-1-4939-6783-4_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
67
Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I. CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res 2016;45:D289-D295. [PMID: 27899584 PMCID: PMC5210570 DOI: 10.1093/nar/gkw1098] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 01/05/2023]  Open
68
Lees JG, Dawson NL, Sillitoe I, Orengo CA. Functional innovation from changes in protein domains and their combinations. Curr Opin Struct Biol 2016;38:44-52. [DOI: 10.1016/j.sbi.2016.05.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
69
Lee D, Das S, Dawson NL, Dobrijevic D, Ward J, Orengo C. Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases. PLoS Comput Biol 2016;12:e1004926. [PMID: 27332861 PMCID: PMC4917113 DOI: 10.1371/journal.pcbi.1004926] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/19/2016] [Indexed: 11/23/2022]  Open
70
Lobb B, Doxey AC. Novel function discovery through sequence and structural data mining. Curr Opin Struct Biol 2016;38:53-61. [DOI: 10.1016/j.sbi.2016.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 01/30/2023]
71
Lam SD, Dawson NL, Das S, Sillitoe I, Ashford P, Lee D, Lehtinen S, Orengo CA, Lees JG. Gene3D: expanding the utility of domain assignments. Nucleic Acids Res 2016;44:D404-9. [PMID: 26578585 PMCID: PMC4702871 DOI: 10.1093/nar/gkv1231] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 12/21/2022]  Open
72
Laskowski RA. Protein Structure Databases. Methods Mol Biol 2016;1415:31-53. [PMID: 27115626 DOI: 10.1007/978-1-4939-3572-7_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
73
Das S, Orengo CA. Protein function annotation using protein domain family resources. Methods 2016;93:24-34. [DOI: 10.1016/j.ymeth.2015.09.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 01/25/2023]  Open
74
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies. J Mol Biol 2015;428:253-267. [PMID: 26585402 PMCID: PMC4751976 DOI: 10.1016/j.jmb.2015.11.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/05/2015] [Accepted: 11/10/2015] [Indexed: 01/28/2023]
75
Das S, Dawson NL, Orengo CA. Diversity in protein domain superfamilies. Curr Opin Genet Dev 2015;35:40-9. [PMID: 26451979 PMCID: PMC4686048 DOI: 10.1016/j.gde.2015.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 01/25/2023]
76
The history of the CATH structural classification of protein domains. Biochimie 2015;119:209-17. [PMID: 26253692 PMCID: PMC4678953 DOI: 10.1016/j.biochi.2015.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/01/2015] [Indexed: 11/21/2022]
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