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ProClass Protein Family Database

C H Wu1, S Shivakumar, H Huang

  • 1Department of Epidemiology/Biomathematics, University of Texas Health Center at Tyler, Tyler, TX 75710, USA. wu@uthct.edu

Nucleic Acids Research
|December 10, 1998
PubMed
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ProClass is a protein family database that integrates sequence data with functional motifs for enhanced classification. This system aids in understanding protein relationships and supports genomic annotation with its high classification rate.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Protein classification is crucial for understanding biological function and evolution.
  • Existing databases often use either global similarity or functional motifs, limiting comprehensive analysis.
  • Integrating diverse data types can improve the accuracy and utility of protein family databases.

Purpose of the Study:

  • To develop and present ProClass, a novel protein family database.
  • To combine PROSITE patterns and PIR superfamilies for a unified classification scheme.
  • To enhance the retrieval of protein family and domain information.

Main Methods:

  • Organizing non-redundant protein sequence entries into families.
  • Utilizing PROSITE patterns and PIR superfamilies for classification.

Related Experiment Videos

  • Integrating motif and global similarity data for a comprehensive scheme.
  • Employing the GeneFIND family identification system for new member detection.

    • Main Results:

    • ProClass currently contains over 120,000 sequence entries.
    • Approximately 60% of entries are classified into about 3,500 families.
    • The database provides links to external protein family, domain, and structural databases.
    • Multiple motif and global alignments are available for PROSITE patterns and PIR superfamilies.

    Conclusions:

    • ProClass effectively reveals domain and family relationships, aiding in the classification of multi-domain proteins.
    • The database's high classification rate supports full-scale genomic annotation.
    • ProClass enhances protein family information retrieval through integrated data and external links.