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DBAli: a database of protein structure alignments.

M A Martí-Renom1, V A Ilyin, A Sali

  • 1Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Ave, New York, NY 10021, USA.

Bioinformatics (Oxford, England)
|August 29, 2001
PubMed
Summary

The DBAli database offers 35,000 protein structure alignments from SCOP and CE. This resource aids in benchmarking alignment methods and exploring protein structure relationships.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • The Database of protein Alignments (DBAli) provides a comprehensive collection of protein structure alignments.
  • It integrates data from the Structural Classification of Proteins (SCOP) and the Combinatorial Extension (CE) algorithm.

Purpose of the Study:

  • To present the DBAli database as a valuable resource for structural bioinformatics.
  • To facilitate the benchmarking of protein sequence and structure alignment methods.

Main Methods:

  • The database contains approximately 35,000 pairwise protein structure alignments.
  • Alignments are derived from the SCOP and CE structural databases.
  • DBAli is linked to visualization tools like Compare3D and ModView.

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Main Results:

  • The database facilitates flexible searching based on protein sequence and structural properties.
  • Users can construct custom subsets of alignments for specific research needs.
  • This enables diverse applications, including method development and validation.

Conclusions:

  • DBAli serves as a crucial resource for researchers in structural biology and bioinformatics.
  • Its comprehensive data and search capabilities support the advancement of protein alignment methodologies.