Domain databases

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Databases discussed during the training

Interpro: a composite databases combining data from several domain databases
Prosite: the best curated domain database

Other domain databases that represent domains by PSMs

HAMAP: a database containing domains from well conserved protein families, represented by PSMs that are manually created by expert curators
PRINTS: a database focussed on describing protein families and specialized in hierarchical definitions from superfamily down to subfamily in order to pin-point specific functions

Other domain databases that represent domains by HMMs

  • Pfam: database containing more divergent domains and motifs
  • SMART
  • PANTHER: tool for characterizing list of proteins with underlying domain database of HMMs based on the divergence of function within protein families
  • PIRSF: domain database of HMMs over full length of proteins meaning that they only use protein families of which members have similar lengths
  • TIGRFAMs: domain database of HMMs based on sets of proteins with the same function
  • Gene3D: domain database of HMMs based on 3D structure using SCOP superfamilies
  • SUPERFAMILY: domain database of HMMs based on 3D structure using CATH superfamilies