Specialized Databases - 11 August 2011 - BioInformatics Pakistan
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Specialized Databases




Generalized DNA, protein and carbohydrate databases
      
  1. Specialized protein databases
    • Proteome databases
      • Proteome analysis (comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms at EBI, UK)
    • Specific protein family databases
      • Proweb (Guide to specific protein families)
      • TRANSFAC (Transcription Factor Database, housed at Biobase)
      • GPCRDB (G-Protein Coupled Receptor Database)
      • PKR (Protein Kinase Resource)
      • ENZYME (Enzyme database at ExPASy, CH)
      • MEROPS (Peptidase database at Sanger Institute, UK)
      • Prolysis (Protease and inhibitors database, Univ of Tours, Fr)
      • CAZy (Carbohydrate-active enZymes at CNRS, Fr)
      • PROMISE (Prostetic groups and Metal Ions in protein active sites database at Scripps Researche Institute, USA)
      • ReLiBase (database system for analysing receptor/ligand complexes deposited in the Protein Data Bank at EBI, UK)
      • IMGT (ImMunoGeneTics database of Igs, TcRs, and MHC molecules at Montpellier, France)
      • REBASE (Restriction enzyme database at New England Biolabs, USA)
    • Protein classification databases
      • CluSTr (Clusters of SWISS-PROT and TrEMBL proteins at EBI, UK)
      • Pfam (Protein families database of alignments and HMMs at the Sanger Centre, UK)
      • TIGRFAMs (Protein families based on HMMs at TIGR, USA)
      • Hits (Protein domain database at ISREC, Switzerland)
      • SCOP (Structural Classification of Proteins according to familiy, superfamily, common fold, and class)
      • CATH (Protein structure classification based on Class, Architecture, Topology, and Homologous superfamilies)
      • BioSpace (Unified sequence-structure classification of proteins, Stanford, USA)
      • LPFC (Library of Protein Family Cores)
      • Dali (Dali Fold classification based on structure-structure alignment of proteins, at Helsinki University, Finland)
      • ENZYME (Enzyme nomenclature database at ExPASy, CH)
      • Enzyme Structures Database (University College London, UK)
      • PRESAGE (Annotated protein structure database at the University of California, Berkeley, USA)
      • CDD (Conserved Domain Database at NCBI, USA)
  2. Specialized structure databases
  3. Pathway databases
    • KEGG(Kyoto Encyclopedia of Genes and Genomes at Kyoto Univ. Jp. or at mirror servers)
    • LIGAND (Chemical database for emzyme reactions at Institute for Chemical Research, Kyoto Univ. Jp)
    • BRITE (Biomolecular Relations in Information, Transmission and Expression, Kyoto Univ., Jp)
    • Boehringer Mannheim - Biochemical pathways (Maintained at ExPASy, Ch)
    • BioCyc (Microbial species-specific integrated pathway/genome database)
    • WIT  (What is There? Integrated pathway/genome database. Registration required)
    • EMP (Database of Enzymes and Metabolic pathways public server
    • UM-BBD (Microbial biocatalysis/biodegradation pathways, University of Minnesota, USA)
    • BRENDA (Enzyme and metabolic database at Univ Cologne, Germany)
    • SRS (Metabolic pathway database search at EBI, UK) 
  4. Microarray databases
    • ArrayExpress (Public repository for microarray based gene expression data at EBI, UK)
    • GEO (Genome Expression Omnibus: Public repository for microarray based gene expression data at NCBI, USA)
  5. 2D-page databases
  6. Lists of databases
    • DBCAT
      (Catalog of more than 500 molecular biology databases at INFOBIOGEN, France )
    • NAR 31 (1) 2003
       (Nucl. Acids Res. biological database issue, papers available through NAR online)
    • NAR 32 (1) 2004
       (Nucl. Acids Res. biological database issue, papers available through NAR online
      )



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