SIMAP--structuring the network of protein similarities

Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, Werner Mewes

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


Protein sequences are the most important source of evolutionary and functional information for new proteins. In order to facilitate the computationally intensive tasks of sequence analysis, the Similarity Matrix of Proteins (SIMAP) database aims to provide a comprehensive and up-to-date dataset of the pre-calculated sequence similarity matrix and sequence-based features like InterPro domains for all proteins contained in the major public sequence databases. As of September 2007, SIMAP covers approximately 17 million proteins and more than 6 million non-redundant sequences and provides a complete annotation based on InterPro 16. Novel features of SIMAP include a new, portlet-based web portal providing multiple, structured views on retrieved proteins and integration of protein clusters and a unique search method for similar domain architectures. Access to SIMAP is freely provided for academic use through the web portal for individuals at through Web Services for programmatic access at

Original languageEnglish
Pages (from-to)D289-92
JournalNucleic Acids Research
Issue numberDatabase issue
Publication statusPublished - Jan 2008


  • Databases, Protein
  • Internet
  • Protein Structure, Tertiary
  • Proteins
  • Sequence Alignment
  • Sequence Analysis, Protein
  • User-Computer Interface
  • Journal Article
  • Research Support, Non-U.S. Gov't


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