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Overview of Enzyme, Protein and Network Databases

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  1. Overview of Enzyme, Protein and Network Databases Cameron Wellock Keck Graduate Institute cwellock@kgi.edu

  2. Protein Databases • Types of Data • Sequence • Function • Recognized Domains • Structural Information & Models • Pathway Information & Models

  3. All-Purpose Databases

  4. Entrez-Protein • Part of a much larger library • Provided through the NIH • Entrez provides Web and programmatic access http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

  5. PIR • Protein Information Resource • Arguably the most comprehensive http://www-nbrf.georgetown.edu/pirwww/dbinfo/pirpsd.html

  6. Swiss-Prot & TrEMBL • A little bit of everything • Swiss-Prot carefully annotated • TrEMBL automatically annotated • Also PROSITE, ENZYME http://us.expasy.org/sprot/

  7. BRENDA • Comprehensive Enzyme Database http://www.brenda.uni-koeln.de/

  8. Structure Databases

  9. PDB • Protein Data Bank • Contains 3D models of proteins • See also PDBSum http://www.rcsb.org/pdb/

  10. Entrez Structure • Another part of Entrez library http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure

  11. Structural Classification DBs

  12. COG • Clusters of Orthologous Groups • 3307 clusters at this time • Based on interspecies comparisons and sequence similarity http://www.ncbi.nlm.nih.gov/COG/

  13. SCOP • Structural Classification of Proteins • Organized in a hierarchy • Based on secondary structure similarities http://scop.berkeley.edu/

  14. CATH • Class, Architecture, Topology, Homologous Superfamily http://www.biochem.ucl.ac.uk/bsm/cath/

  15. Functional Classification Databases

  16. ENZYME • Nomenclature database • Hierarchical organization http://us.expasy.org/enzyme/

  17. KEGG • Kyoto Encyclopedia of Genes and Genomes • Its own classification scheme (KO) • Massive pathway maps • Links into COGS and ENZYME • Has a SOAP-based programmatic interface http://www.genome.ad.jp/kegg/

  18. Domain Databases

  19. InterPro • A large aggregated database, uses many sources in its search http://www.ebi.ac.uk/interpro/

  20. PROSITE • Also part of ExPASy http://us.expasy.org/prosite/

  21. Special-Purpose Databases

  22. HPRD • Human Protein Reference Database http://www.hprd.org/

  23. Commercial Databases • Incyte BioKnowledge (http://www.incyte.com/control/researchproducts/insilico/proteome)

  24. Places to Look http://bmbsgi10.leeds.ac.uk/moldb.html http://www.infobiogen.fr/services/dbcat/