Orengo C - Search Results

1

ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.

Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. Vallat B, et al. Among authors: orengo c. J Mol Biol. 2023 Jul 15;435(14):168021. doi: 10.1016/j.jmb.2023.168021. Epub 2023 Feb 23. J Mol Biol. 2023. PMID: 36828268 Free PMC article.

2

Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction.

Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I. Orengo CA, et al. Proteins. 1999;Suppl 3:149-70. doi: 10.1002/(sici)1097-0134(1999)37:3+<149::aid-prot20>3.3.co;2-8. Proteins. 1999. PMID: 10526364

3

Review: what can structural classifications reveal about protein evolution?

Orengo CA, Sillitoe I, Reeves G, Pearl FM. Orengo CA, et al. J Struct Biol. 2001 May-Jun;134(2-3):145-65. doi: 10.1006/jsbi.2001.4398. J Struct Biol. 2001. PMID: 11551176 Review.

4

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.

Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA. Cuff AL, et al. Among authors: orengo ca. Nucleic Acids Res. 2009 Jan;37(Database issue):D310-4. doi: 10.1093/nar/gkn877. Epub 2008 Nov 7. Nucleic Acids Res. 2009. PMID: 18996897 Free PMC article.

5

FLORA: a novel method to predict protein function from structure in diverse superfamilies.

Redfern OC, Dessailly BH, Dallman TJ, Sillitoe I, Orengo CA. Redfern OC, et al. Among authors: orengo ca. PLoS Comput Biol. 2009 Aug;5(8):e1000485. doi: 10.1371/journal.pcbi.1000485. Epub 2009 Aug 28. PLoS Comput Biol. 2009. PMID: 19714201 Free PMC article.

6

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.

Furnham N, Sillitoe I, Holliday GL, Cuff AL, Rahman SA, Laskowski RA, Orengo CA, Thornton JM. Furnham N, et al. Nucleic Acids Res. 2012 Jan;40(Database issue):D776-82. doi: 10.1093/nar/gkr852. Epub 2011 Oct 17. Nucleic Acids Res. 2012. PMID: 22006843 Free PMC article.

7

Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.

Furnham N, Sillitoe I, Holliday GL, Cuff AL, Laskowski RA, Orengo CA, Thornton JM. Furnham N, et al. PLoS Comput Biol. 2012;8(3):e1002403. doi: 10.1371/journal.pcbi.1002403. Epub 2012 Mar 1. PLoS Comput Biol. 2012. PMID: 22396634 Free PMC article.

8

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.

Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA. Lees JG, et al. Among authors: orengo ca. Nucleic Acids Res. 2014 Jan;42(Database issue):D240-5. doi: 10.1093/nar/gkt1205. Epub 2013 Nov 21. Nucleic Acids Res. 2014. PMID: 24270792 Free PMC article.

9

CATH: comprehensive structural and functional annotations for genome sequences.

Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA. Sillitoe I, et al. Nucleic Acids Res. 2015 Jan;43(Database issue):D376-81. doi: 10.1093/nar/gku947. Epub 2014 Oct 27. Nucleic Acids Res. 2015. PMID: 25348408 Free PMC article.

10

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.

Das S, Lee D, Sillitoe I, Dawson NL, Lees JG, Orengo CA. Das S, et al. Bioinformatics. 2015 Nov 1;31(21):3460-7. doi: 10.1093/bioinformatics/btv398. Epub 2015 Jul 2. Bioinformatics. 2015. PMID: 26139634 Free PMC article.

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