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Title: PROCOGNATE: a cognate ligand domain mapping for enzymes

Abstract

PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file. This article gives an overview of the database and its generation and presents a new website front end, as well as recent increased coverage in our dataset via inclusion of Pfam domains. We also describe navigation of the website and its features. The current version (1.3) of PROCOGNATE covers 4123, 4536, 5876 structures and 377, 326, 695 superfamilies/families in CATH, SCOP and Pfam, respectively. PROCOGNATE can be accessed at: http://www.ebi.ac.uk/ thornton-srv/databases/procognate/

Authors:
 [1];  [2];  [1]
+ Show Author Affiliations
  1. European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom). Wellcome Trust Genome Campus
  2. King's College, London (United Kingdom). Randall Division of Cell and Molecular Biophysics
Publication Date:
Research Org.:
European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH)
OSTI Identifier:
1625427
Grant/Contract Number:  
W-31-109-ENG38; GM62414
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 36; Journal Issue: suppl_1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats

Bashton, M., Nobeli, I., and Thornton, J. M. PROCOGNATE: a cognate ligand domain mapping for enzymes. United States: N. p., 2007. Web. doi:10.1093/nar/gkm611.
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Bashton, M., Nobeli, I., & Thornton, J. M. PROCOGNATE: a cognate ligand domain mapping for enzymes. United States. https://doi.org/10.1093/nar/gkm611
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Bashton, M., Nobeli, I., and Thornton, J. M. Fri . "PROCOGNATE: a cognate ligand domain mapping for enzymes". United States. https://doi.org/10.1093/nar/gkm611. https://www.osti.gov/servlets/purl/1625427.
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@article{osti_1625427,
title = {PROCOGNATE: a cognate ligand domain mapping for enzymes},
author = {Bashton, M. and Nobeli, I. and Thornton, J. M.},
abstractNote = {PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file. This article gives an overview of the database and its generation and presents a new website front end, as well as recent increased coverage in our dataset via inclusion of Pfam domains. We also describe navigation of the website and its features. The current version (1.3) of PROCOGNATE covers 4123, 4536, 5876 structures and 377, 326, 695 superfamilies/families in CATH, SCOP and Pfam, respectively. PROCOGNATE can be accessed at: http://www.ebi.ac.uk/ thornton-srv/databases/procognate/},
doi = {10.1093/nar/gkm611},
journal = {Nucleic Acids Research},
number = suppl_1,
volume = 36,
place = {United States},
year = {Fri Aug 24 00:00:00 EDT 2007},
month = {Fri Aug 24 00:00:00 EDT 2007}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1093/nar/gkm611
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Works referenced in this record:

PatMatch: a program for finding patterns in peptide and nucleotide sequences
journal, July 2005

  • Yan, T.; Yoo, D.; Berardini, T. Z.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki368

The ENZYME database in 2000
journal, January 2000

MSDsite: A database search and retrieval system for the analysis and viewing of bound ligands and active sites
journal, October 2004

  • Golovin, Adel; Dimitropoulos, Dimitris; Oldfield, Tom
  • Proteins: Structure, Function, and Bioinformatics, Vol. 58, Issue 1
  • DOI: 10.1002/prot.20288

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids
journal, December 2004

  • Laskowski, R. A.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki001

Announcing the worldwide Protein Data Bank
journal, December 2003

  • Berman, Helen; Henrick, Kim; Nakamura, Haruki
  • Nature Structural & Molecular Biology, Vol. 10, Issue 12
  • DOI: 10.1038/nsb1203-980

Cognate Ligand Domain Mapping for Enzymes
journal, December 2006

  • Bashton, Matthew; Nobeli, Irene; Thornton, Janet M.
  • Journal of Molecular Biology, Vol. 364, Issue 4
  • DOI: 10.1016/j.jmb.2006.09.041

Ligand Depot: a data warehouse for ligands bound to macromolecules
journal, April 2004

The Universal Protein Resource (UniProt)
journal, January 2007

  • Bairoch, Amos; Bougueleret, Lydie; Altairac, Severine
  • Nucleic Acids Research, Vol. 35, Issue Database, p. D193-D197
  • DOI: 10.1093/nar/gkl929

Pfam: clans, web tools and services
journal, January 2006

The Biomolecular Interaction Network Database and related tools 2005 update
journal, December 2004

  • Alfarano, C.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki051

DrugBank: a comprehensive resource for in silico drug discovery and exploration
journal, January 2006

The Chemistry Development Kit (CDK):  An Open-Source Java Library for Chemo- and Bioinformatics
journal, February 2003

  • Steinbeck, Christoph; Han, Yongquan; Kuhn, Stefan
  • Journal of Chemical Information and Computer Sciences, Vol. 43, Issue 2
  • DOI: 10.1021/ci025584y

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999

  • Ogata, H.; Goto, S.; Sato, K.
  • Nucleic Acids Research, Vol. 27, Issue 1
  • DOI: 10.1093/nar/27.1.29

PDBLIG:  Classification of Small Molecular Protein Binding in the Protein Data Bank
journal, July 2004

  • Chalk, Andrew J.; Worth, Catherine L.; Overington, John P.
  • Journal of Medicinal Chemistry, Vol. 47, Issue 15
  • DOI: 10.1021/jm040804f

Databases for Protein–Ligand Complexes
journal, November 1998

  • Hendlich, Manfred
  • Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 6
  • DOI: 10.1107/S0907444998007124

The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics.
journal, May 2003

Cognate Ligand Domain Mapping for Enzymes
journal, December 2006

  • Bashton, Matthew; Nobeli, Irene; Thornton, Janet M.
  • Journal of Molecular Biology, Vol. 364, Issue 4
  • DOI: 10.1016/j.jmb.2006.09.041

Announcing the worldwide Protein Data Bank
journal, December 2003

  • Berman, Helen; Henrick, Kim; Nakamura, Haruki
  • Nature Structural & Molecular Biology, Vol. 10, Issue 12
  • DOI: 10.1038/nsb1203-980

Ligand Depot: a data warehouse for ligands bound to macromolecules
journal, April 2004

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999

  • Ogata, H.; Goto, S.; Sato, K.
  • Nucleic Acids Research, Vol. 27, Issue 1
  • DOI: 10.1093/nar/27.1.29

The ENZYME database in 2000
journal, January 2000

PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids
journal, December 2004

  • Laskowski, R. A.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki001

The Biomolecular Interaction Network Database and related tools 2005 update
journal, December 2004

  • Alfarano, C.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki051

E-MSD: an integrated data resource for bioinformatics
journal, December 2004

  • Velankar, S.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki058

DrugBank: a comprehensive resource for in silico drug discovery and exploration
journal, January 2006

The Universal Protein Resource (UniProt)
journal, January 2007

  • Bairoch, Amos; Bougueleret, Lydie; Altairac, Severine
  • Nucleic Acids Research, Vol. 35, Issue Database, p. D193-D197
  • DOI: 10.1093/nar/gkl929
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    Works referencing / citing this record:

    Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions
    journal, December 2018

    • Kobren, Shilpa Nadimpalli; Singh, Mona
    • Nucleic Acids Research, Vol. 47, Issue 2
    • DOI: 10.1093/nar/gky1224

    Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus
    journal, January 2017

    • Mock, Thomas; Otillar, Robert P.; Strauss, Jan
    • Nature, Vol. 541, Issue 7638
    • DOI: 10.1038/nature20803

    Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding
    journal, September 2012

    Systematic domain-based aggregation of protein structures highlights DNA-, RNA-, and other ligand-binding positions
    posted_content, August 2018

    • Kobren, Shilpa Nadimpalli; Singh, Mona
    • Nucleic Acids Research
    • DOI: 10.1101/394494

    IsoCleft Finder – a web-based tool for the detection and analysis of protein binding-site geometric and chemical similarities
    journal, January 2013

    iPfam: a database of protein family and domain interactions found in the Protein Data Bank
    journal, December 2013

    • Finn, Robert D.; Miller, Benjamin L.; Clements, Jody
    • Nucleic Acids Research, Vol. 42, Issue D1
    • DOI: 10.1093/nar/gkt1210

    Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
    journal, September 2014

    • Anand, Praveen; Chandra, Nagasuma
    • Scientific Reports, Vol. 4, Issue 1
    • DOI: 10.1038/srep06356

    Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
    journal, January 2015

    • Currin, Andrew; Swainston, Neil; Day, Philip J.
    • Chemical Society Reviews, Vol. 44, Issue 5
    • DOI: 10.1039/c4cs00351a

    The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis
    journal, January 2012

    • Caetano-Anollés, Gustavo; Kim, Kyung Mo; Caetano-Anollés, Derek
    • Journal of Molecular Evolution, Vol. 74, Issue 1-2
    • DOI: 10.1007/s00239-011-9480-1

    Protein Conformational Diversity Modulates Sequence Divergence
    journal, March 2012

    • Juritz, Ezequiel; Palopoli, Nicolas; Fornasari, Maria Silvina
    • Molecular Biology and Evolution, Vol. 30, Issue 1
    • DOI: 10.1093/molbev/mss080

    PepX: a structural database of non-redundant protein–peptide complexes
    journal, October 2009

    • Vanhee, Peter; Reumers, Joke; Stricher, Francois
    • Nucleic Acids Research, Vol. 38, Issue suppl_1
    • DOI: 10.1093/nar/gkp893

    Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
    journal, September 2014

    • Anand, Praveen; Chandra, Nagasuma
    • Scientific Reports, Vol. 4, Issue 1
    • DOI: 10.1038/srep06356

    Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
    journal, January 2015

    • Currin, Andrew; Swainston, Neil; Day, Philip J.
    • Chemical Society Reviews, Vol. 44, Issue 5
    • DOI: 10.1039/c4cs00351a

    Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding
    journal, September 2012

    SuperSite: dictionary of metabolite and drug binding sites in proteins
    journal, January 2009

    • Bauer, R. A.; Gunther, S.; Jansen, D.
    • Nucleic Acids Research, Vol. 37, Issue Database
    • DOI: 10.1093/nar/gkn618

    @TOME-2: a new pipeline for comparative modeling of protein-ligand complexes
    journal, May 2009

    • Pons, J. -L.; Labesse, G.
    • Nucleic Acids Research, Vol. 37, Issue Web Server
    • DOI: 10.1093/nar/gkp368

    PepX: a structural database of non-redundant protein–peptide complexes
    journal, October 2009

    • Vanhee, Peter; Reumers, Joke; Stricher, Francois
    • Nucleic Acids Research, Vol. 38, Issue suppl_1
    • DOI: 10.1093/nar/gkp893

    firestar —advances in the prediction of functionally important residues
    journal, June 2011

    • Lopez, Gonzalo; Maietta, Paolo; Rodriguez, Jose Manuel
    • Nucleic Acids Research, Vol. 39, Issue suppl_2
    • DOI: 10.1093/nar/gkr437

    iPfam: a database of protein family and domain interactions found in the Protein Data Bank
    journal, December 2013

    • Finn, Robert D.; Miller, Benjamin L.; Clements, Jody
    • Nucleic Acids Research, Vol. 42, Issue D1
    • DOI: 10.1093/nar/gkt1210

    Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions
    journal, December 2018

    • Kobren, Shilpa Nadimpalli; Singh, Mona
    • Nucleic Acids Research, Vol. 47, Issue 2
    • DOI: 10.1093/nar/gky1224

    Identification of NAD interacting residues in proteins
    journal, March 2010

    The human "magnesome": detecting magnesium binding sites on human proteins
    journal, September 2012

    On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions
    journal, June 2012

    • Juritz, Ezequiel; Fornasari, Maria Silvina; Martelli, Pier Luigi
    • BMC Genomics, Vol. 13, Issue S4
    • DOI: 10.1186/1471-2164-13-s4-s5

    FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies
    journal, August 2009

    • Redfern, Oliver C.; Dessailly, Benoît H.; Dallman, Timothy J.
    • PLoS Computational Biology, Vol. 5, Issue 8
    • DOI: 10.1371/journal.pcbi.1000485

    Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome
    journal, June 2013

    Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests
    journal, January 2014

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