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GIS: a comprehensive source for protein structure similarities.

Aysam Guerler1, Ernst-Walter Knapp

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A new web service, GANGSTA+ Internet Services (GIS), offers protein structure alignment. It uses the GANGSTA+ algorithm to find non-sequential structural similarities, aiding in the discovery of novel protein folds.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • The GANGSTA+ algorithm identifies non-sequential structural analogs in proteins, even those with shuffled sequences.
  • It is particularly useful for detecting similarities in proteins with novel folds by disregarding chain connectivity.

Purpose of the Study:

  • To provide a public web-based service for accessing protein structure alignments generated by GANGSTA+.
  • To enable browsing of the ASTRAL40 database and analysis of protein structure families using GANGSTA+.

Main Methods:

  • An all-against-all comparison of the ASTRAL40 database (>10,000 protein domains) using the GANGSTA+ algorithm.
  • Development of the GANGSTA+ Internet Services (GIS) web platform to host and query these alignments.

Main Results:

  • Generation of approximately 55 million protein structure alignments from the ASTRAL40 database.
  • The GIS service allows users to browse alignments, analyze SCOP classification families, and perform custom comparisons.

Conclusions:

  • GIS provides a valuable resource for researchers studying protein structure evolution and function.
  • The service facilitates the identification of non-sequential structural similarities, expanding our understanding of protein folds.