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Items: 1 to 20 of 97

1.

Genome3D: exploiting structure to help users understand their sequences.

Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, Murzin AG, Ochoa-Montaño B, Oates ME, Punta M, Rackham OJ, Stahlhacke J, Sternberg MJ, Velankar S, Orengo C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D382-6. doi: 10.1093/nar/gku973. Epub 2014 Oct 27.

2.

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D499-507. doi: 10.1093/nar/gks1266. Epub 2012 Nov 30.

3.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D240-5. doi: 10.1093/nar/gkt1205. Epub 2013 Nov 21.

4.

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA.

Nucleic Acids Res. 2013 Jan;41(Database issue):D490-8. doi: 10.1093/nar/gks1211. Epub 2012 Nov 29.

5.

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.

Nucleic Acids Res. 2015 Jan;43(Database issue):D376-81. doi: 10.1093/nar/gku947. Epub 2014 Oct 27.

6.

Gene3D: expanding the utility of domain assignments.

Lam SD, Dawson NL, Das S, Sillitoe I, Ashford P, Lee D, Lehtinen S, Orengo CA, Lees JG.

Nucleic Acids Res. 2016 Jan 4;44(D1):D404-9. doi: 10.1093/nar/gkv1231. Epub 2015 Nov 17.

7.

Gene3D: modelling protein structure, function and evolution.

Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D281-4.

8.

EVEREST: a collection of evolutionary conserved protein domains.

Portugaly E, Linial N, Linial M.

Nucleic Acids Res. 2007 Jan;35(Database issue):D241-6. Epub 2006 Nov 11.

9.

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.

10.

SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences.

Han A, Kang HJ, Cho Y, Lee S, Kim YJ, Gong S.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W642-4.

11.
12.

SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.

Arnold R, Goldenberg F, Mewes HW, Rattei T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D279-84. doi: 10.1093/nar/gkt970. Epub 2013 Oct 27.

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.

MyHits: a new interactive resource for protein annotation and domain identification.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Falquet L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W332-5.

15.

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.

Bioinformatics. 2015 Nov 1;31(21):3460-7. doi: 10.1093/bioinformatics/btv398. Epub 2015 Jul 2. Erratum in: Bioinformatics. 2016 Sep 15;32(18):2889.

16.

Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.

Lees J, Yeats C, Perkins J, Sillitoe I, Rentzsch R, Dessailly BH, Orengo C.

Nucleic Acids Res. 2012 Jan;40(Database issue):D465-71. doi: 10.1093/nar/gkr1181. Epub 2011 Dec 1. Erratum in: Nucleic Acids Res. 2012 May;40(10):4725.

17.

Gene3D: merging structure and function for a Thousand genomes.

Lees J, Yeats C, Redfern O, Clegg A, Orengo C.

Nucleic Acids Res. 2010 Jan;38(Database issue):D296-300. doi: 10.1093/nar/gkp987. Epub 2009 Nov 11.

18.

SMART 7: recent updates to the protein domain annotation resource.

Letunic I, Doerks T, Bork P.

Nucleic Acids Res. 2012 Jan;40(Database issue):D302-5. doi: 10.1093/nar/gkr931. Epub 2011 Nov 3.

19.

CDD: a conserved domain database for interactive domain family analysis.

Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH.

Nucleic Acids Res. 2007 Jan;35(Database issue):D237-40. Epub 2006 Nov 29.

20.

ADDA: a domain database with global coverage of the protein universe.

Heger A, Wilton CA, Sivakumar A, Holm L.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D188-91.

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