ExPASy of the Swiss Institute of Bioinformatics (http://ca.expasy.org/)

Description of Databases

SWISS-PROT
  • protein sequence database which provides annotations (such as the description of the function of the protein, its domains structure, post-translational modifications, variants, etc.)
  • cross-referenced with sequence related databases (notably nucleic acid sequence, protein sequences, and protein tertiary structure databases)
  • search by ID, description, gene name, organism, protein name, or AC (accession number)
PROSITE
  • a database of protein families and domains
  • consists of biologically significant sites, patterns and profiles to identify the protein family
  • search by description, entry name, author, citation, or a full text search (keywords)
SWISS 2D-PAGE
  • a database of 2D polyacrylamide gel electrophoresis reference maps
  • contains mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition) and bibliographical references for a protein
  • contains 2D-PAGE images of experimentally determined locations as well as theoretical regions computed from sequence
  • cross-references to Medline and other federated 2-DE databases
  • search by description (DE lines), entry name (ID), gene name (GN) or species (OS) using the link called "by description…."
  • search by AC number (accession number), author, spot serial number, or full text (keyword)
  • The third link is "clicking on a spot" has images of 2D-PAGE of common cells
SWISS 3D-IMAGE
  • an image database of biological macromolecules with known three-dimensional structure
  • contains mostly images of experimentally elucidated structures but also provides views of well accepted theoretical protein models
  • images are provided in several formats; both mono and stereo pictures are generally available
  • search by description, identification (any word in the DE, OS, KW and ID lines, or PDB code), or by AC (accession number)
ENZYME
  • database of information relative to the nomenclature of enzymes
  • it is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB)
  • contains the following data for each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided:
    • EC number
    • Recommended name
    • Alternative names (if any)
    • Catalytic activity
    • Cofactors (if any)
    • Pointers to the SWISS-PROT protein sequence
    • Pointers to human disease(s) associated with a deficiency of the enzyme (if any)
  • search by EC number, enzyme class, description (official or alternative name), chemical compound, cofactor, or keyword search
  • the cofactor search brings up a list of links corresponding to the appropriate cofactor
SeqAnalRef
  • database of bibliographical references relative to papers dealing with sequence analysis
  • references to articles of mathematical and computer analysis of biomolecular sequences
  • search by keyword, reference identifier, author, citation, or full text (keyword)

Other Useful Features On This Site

SWISS-SHOP

This feature allows you to search the weekly updates to the SWISS-PROT database. Only the weekly updates are searched. This is
done by filling out the search form on the SWISS-SHOP page, accessed by the link under the Education and Services heading in the
main page. The results are returned to you by email. There is also a link to where you can ask a question via email called "Ask
Questions". There are 2 search options, by a sequence/pattern based search or a keyword search. Follow the directions listed for each
type of search. Other options include what type of information you want sent back to you and a password option that allows you to
save you search fields in case you want to edit it or do a new search with slightly different parameters.
Keep in mind is THERE IS NO GUARANTEE THAT REPLIES WILL BE PROMPT SO BE PREPARED TO WAIT.

LINKS

This site is a good launch pad for other information as it provides links to other useful sites and major servers.
The following is a list of the more useful links:

Tools and Software Packages

This page contains almost all the online software for getting information about proteins and DNA. A description of each of the tools can
be found HERE.

Proteomics tools:

Boehringer Mannheim's Biochemical Pathways

Links to lists of molecular biology resources