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

Frances Pearl; Annabel Todd; Ian Sillitoe; Mark Dibley; Oliver Redfern; Tony Lewis; Christopher Bennett; Russell Marsden; Alistair Grant; David Lee; Adrian Akpor; Michael Maibaum; Andrew Harrison; Timothy Dallman; Gabrielle Reeves; Ilhem Diboun; Sarah Addou; Stefano Lise; Caroline Johnston; Antonio Sillero; Janet Thornton; Christine Orengo

doi:10.1093/nar/gki024

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

Frances Pearl, Annabel Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony Lewis, Christopher Bennett, Russell Marsden, Alistair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew Harrison, Timothy Dallman, Gabrielle Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio SilleroJanet Thornton, Christine Orengo

IRAS OH Epidemiology Microbial Agents

Goldsmiths University London, University of London

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616,470 domain sequences classified into 23,876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.

Original language	English
Pages (from-to)	D247-51
Journal	Nucleic Acids Research
Volume	33
Issue number	Database issue
DOIs	https://doi.org/10.1093/nar/gki024
Publication status	Published - 1 Jan 2005

Keywords

Databases, Nucleic Acid
Databases, Protein/statistics & numerical data
Genomics
Internet
Protein Structure, Tertiary
Proteins/classification
Sequence Analysis, Protein
Sequence Homology, Amino Acid
Systems Integration
User-Computer Interface

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10.1093/nar/gki024

Cite this

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., ... Orengo, C. (2005). The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Research, 33(Database issue), D247-51. https://doi.org/10.1093/nar/gki024

@article{fcf3d11a913946b78a42fa59a608d0de,

title = "The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis",

abstract = "The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616,470 domain sequences classified into 23,876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10\% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.",

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author = "Frances Pearl and Annabel Todd and Ian Sillitoe and Mark Dibley and Oliver Redfern and Tony Lewis and Christopher Bennett and Russell Marsden and Alistair Grant and David Lee and Adrian Akpor and Michael Maibaum and Andrew Harrison and Timothy Dallman and Gabrielle Reeves and Ilhem Diboun and Sarah Addou and Stefano Lise and Caroline Johnston and Antonio Sillero and Janet Thornton and Christine Orengo",

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doi = "10.1093/nar/gki024",

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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 2005, 'The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis', Nucleic Acids Research, vol. 33, no. Database issue, pp. D247-51. https://doi.org/10.1093/nar/gki024

TY - JOUR

T1 - The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis

AU - Pearl, Frances

AU - Todd, Annabel

AU - Sillitoe, Ian

AU - Dibley, Mark

AU - Redfern, Oliver

AU - Lewis, Tony

AU - Bennett, Christopher

AU - Marsden, Russell

AU - Grant, Alistair

AU - Lee, David

AU - Akpor, Adrian

AU - Maibaum, Michael

AU - Harrison, Andrew

AU - Dallman, Timothy

AU - Reeves, Gabrielle

AU - Diboun, Ilhem

AU - Addou, Sarah

AU - Lise, Stefano

AU - Johnston, Caroline

AU - Sillero, Antonio

AU - Thornton, Janet

AU - Orengo, Christine

PY - 2005/1/1

Y1 - 2005/1/1

N2 - The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616,470 domain sequences classified into 23,876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.

AB - The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616,470 domain sequences classified into 23,876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.

KW - Databases, Nucleic Acid

KW - Databases, Protein/statistics & numerical data

KW - Genomics

KW - Internet

KW - Protein Structure, Tertiary

KW - Proteins/classification

KW - Sequence Analysis, Protein

KW - Sequence Homology, Amino Acid

KW - Systems Integration

KW - User-Computer Interface

U2 - 10.1093/nar/gki024

DO - 10.1093/nar/gki024

M3 - Article

C2 - 15608188

SN - 0305-1048

VL - 33

SP - D247-51

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -

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

Abstract

Keywords

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