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Items: 1 to 20 of 115

1.

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.

Nucleic Acids Res. 2012 Jan;40(Database issue):D776-82. doi: 10.1093/nar/gkr852. Epub 2011 Oct 17.

2.

FunTree: advances in a resource for exploring and contextualising protein function evolution.

Sillitoe I, Furnham N.

Nucleic Acids Res. 2016 Jan 4;44(D1):D317-23. doi: 10.1093/nar/gkv1274. Epub 2015 Nov 20.

3.

Evolution of function in protein superfamilies, from a structural perspective.

Todd AE, Orengo CA, Thornton JM.

J Mol Biol. 2001 Apr 6;307(4):1113-43.

PMID:
11286560
4.

The Structure-Function Linkage Database.

Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC.

Nucleic Acids Res. 2014 Jan;42(Database issue):D521-30. doi: 10.1093/nar/gkt1130. Epub 2013 Nov 23.

5.

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.

Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM.

Nucleic Acids Res. 2007 Jan;35(Database issue):D515-20. Epub 2006 Nov 1.

6.

MACiE: exploring the diversity of biochemical reactions.

Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9. doi: 10.1093/nar/gkr799. Epub 2011 Nov 3.

7.

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.

Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D327-31.

8.

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.

PLoS Comput Biol. 2012;8(3):e1002403. doi: 10.1371/journal.pcbi.1002403. Epub 2012 Mar 1.

9.

Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies.

Nagao C, Nagano N, Mizuguchi K.

Proteins. 2010 Aug 1;78(10):2369-84. doi: 10.1002/prot.22750.

PMID:
20544971
10.

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.

Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 6.

11.

The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues.

Bray JE, Todd AE, Pearl FM, Thornton JM, Orengo CA.

Protein Eng. 2000 Mar;13(3):153-65.

PMID:
10775657
12.

PASS2: an automated database of protein alignments organised as structural superfamilies.

Bhaduri A, Pugalenthi G, Sowdhamini R.

BMC Bioinformatics. 2004 Apr 2;5:35.

13.

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.

Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA.

Nucleic Acids Res. 2007 Jan;35(Database issue):D291-7. Epub 2006 Nov 29.

14.

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.

Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D247-51.

15.

PASS2: a semi-automated database of protein alignments organised as structural superfamilies.

Mallika V, Bhaduri A, Sowdhamini R.

Nucleic Acids Res. 2002 Jan 1;30(1):284-8.

16.

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.

Yeats C, Lees J, Carter P, Sillitoe I, Orengo C.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W546-50. doi: 10.1093/nar/gkr438. Epub 2011 Jun 6.

17.

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA.

J Mol Biol. 2016 Jan 29;428(2 Pt A):253-267. doi: 10.1016/j.jmb.2015.11.010. Epub 2015 Nov 14.

18.

S4: structure-based sequence alignments of SCOP superfamilies.

Casbon J, Saqi MA.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D219-22.

19.

Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

Sillitoe I, Lewis T, Orengo C.

Curr Protoc Bioinformatics. 2015 Jun 19;50:1.28.1-21. doi: 10.1002/0471250953.bi0128s50.

PMID:
26087950
20.

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.

Porter CT, Bartlett GJ, Thornton JM.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D129-33.

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