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ProClass protein family database.

H Huang1, C Xiao, C H Wu

  • 1Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.

Nucleic Acids Research
|December 11, 1999
PubMed
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ProClass organizes protein sequences into families using global similarities and functional motifs. This protein family database aids in genomic annotation by revealing domain relationships and classifying proteins.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Protein sequence databases like PIR-International and SWISS-PROT contain vast amounts of biological data.
  • Classifying proteins into families is crucial for understanding their function and evolutionary relationships.
  • Existing classification methods may not fully capture the complexity of multi-domain proteins or novel sequence families.

Purpose of the Study:

  • To develop and present ProClass, a comprehensive protein family database.
  • To integrate global sequence similarities with functional motifs for a unified classification system.
  • To enhance the discoverability and annotation of protein sequences, particularly multi-domain proteins.

Main Methods:

  • ProClass integrates data from PIR-Superfamilies and PROSITE patterns.

Related Experiment Videos

  • It utilizes a GeneFIND family identification system to detect new members.
  • Sequence entries are classified based on combined global similarities and functional motifs.

    • Main Results:

    • The ProClass database contains over 155,000 non-redundant sequence entries.
    • Approximately 60% (92,000 entries) are classified into around 6,000 families.
    • The motif collection includes over 72,000 motif sequences and 1,300 multiple alignments, identifying over 21,000 new matches.

    Conclusions:

    • ProClass provides a high classification rate and comprehensive family relationships.
    • The database facilitates the revelation of domain and family relationships.
    • ProClass supports full-scale genomic annotation and is available via a WWW server.