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EXProt--a database for EXPerimentally verified Protein functions.

Björn M Ursing1, Frank H J van Enckevort, Jack A M Leunissen

  • 1Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands. ursing@cmbi.kun.nl

In Silico Biology
|January 31, 2002
PubMed
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EXProt is a new database featuring experimentally verified protein functions. This non-redundant resource aids researchers by providing curated protein sequence and functional annotation data.

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Experimental verification of protein function is crucial for understanding biological systems.
  • Existing databases may contain redundant or unverified functional annotations.
  • A centralized, curated resource for experimentally verified protein functions is needed.

Purpose of the Study:

  • To introduce EXProt, a novel, non-redundant database of experimentally verified protein functions.
  • To provide researchers with easy access to reliable protein functional data.
  • To facilitate the study of prokaryotic proteins and their functions.

Main Methods:

  • Compilation of protein sequences with experimentally verified functions from EMBL Nucleotide Sequence Database and Pseudomonas Community Annotation Project.

Related Experiment Videos

  • Inclusion of unique identifiers, organism details, protein sequences, and functional annotations.
  • Development of a web interface for database access and BLAST searches.
  • Indexing entries in SRS for keyword-based searching.

    • Main Results:

    • EXProt contains 3976 entries from EMBL and 375 from PseudoCAP, all with experimentally verified functions.
    • Each entry includes organism, sequence, functional annotation, original database link, gene name, and PubMed links.
    • A web page offers database details and BLAST search capabilities (blastp & blastx).
    • Database is searchable via keywords through SRS.

    Conclusions:

    • EXProt serves as a valuable, non-redundant resource for experimentally verified protein functions.
    • The database enhances accessibility to curated functional information for prokaryotic proteins.
    • EXProt supports further research in molecular biology and bioinformatics through its comprehensive data and search functionalities.