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ArchDB: automated protein loop classification as a tool for structural genomics.

Jordi Espadaler1, Narcis Fernandez-Fuentes, Antonio Hermoso

  • 1Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

Nucleic Acids Research
|December 19, 2003
PubMed
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ArchDB is a new database classifying protein structural motifs, which are key to protein function. This resource helps researchers link protein structure, function, and sequence data.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Protein function annotation is challenging due to large-scale genomics data.
  • Protein structure is often encoded in local sequences and super-secondary structural motifs.
  • Protein loops are critical for protein function.

Purpose of the Study:

  • To present ArchDB, a novel database for classifying structural motifs.
  • To facilitate the retrieval of functional information from protein structures.
  • To enable searching for motifs within specific SCOP classifications or by keywords.

Main Methods:

  • Development of ArchDB, a database classifying structural motifs (loop + bracing secondary structures).
  • Classification of 12,665 super-secondary elements into 1496 motif subclasses.

Related Experiment Videos

  • Implementation of search functionalities based on common motifs, SCOP classifications, and keywords.

    • Main Results:

    • ArchDB contains 12,665 super-secondary structural elements.
    • These elements are organized into 1496 distinct motif subclasses.
    • The database enables efficient retrieval and searching of structural motif information.

    Conclusions:

    • ArchDB provides a valuable resource for understanding the relationship between protein structure and function.
    • The classification of structural motifs aids in functional annotation and sequence-structure analysis.
    • ArchDB serves as a key tool for researchers in structural genomics and protein science.