ProDom: automated clustering of homologous domains

Brief Bioinform. 2002 Sep;3(3):246-51. doi: 10.1093/bib/3.3.246.


The ProDom database is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases. An associated database, ProDom-CG, has been derived as a restriction of ProDom to completely sequenced genomes. The ProDom construction method is based on iterative PSI-BLAST searches and multiple alignments are generated for each domain family. The ProDom web server provides the user with a set of tools to visualise multiple alignments, phylogenetic trees and domain architectures of proteins, as well as a BLAST-based server to analyse new sequences for homologous domains. The comprehensive nature of ProDom makes it particularly useful to help sustain the growth of InterPro.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein*
  • Genome
  • Information Services
  • Internet
  • Models, Molecular
  • Phylogeny
  • Protein Structure, Tertiary*
  • Proteins / chemistry*
  • Proteins / classification
  • Sequence Alignment
  • Sequence Analysis, Protein
  • User-Computer Interface


  • Proteins