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Related Experiment Videos

A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE)

I N Shindyalov1, P E Bourne

  • 1San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Nucleic Acids Research
|January 11, 2000
PubMed
Summary
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The Combinatorial Extension (CE) algorithm identifies structurally similar proteins, aiding in the annotation of proteins with unknown functions. This method infers biological relationships not evident from sequence analysis alone.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • The rapid growth in structural genomics yields numerous protein structures with undetermined functions.
  • Inferring biological function from protein structure is crucial for understanding biological processes.
  • Sequence-based comparisons alone are often insufficient for functional inference.

Purpose of the Study:

  • To present the Combinatorial Extension (CE) database and algorithm for identifying structure-structure relationships.
  • To highlight the utility of CE in annotating protein structures with unknown functions.
  • To provide tools for analyzing and visualizing protein structural similarities.

Main Methods:

  • The Combinatorial Extension (CE) algorithm compares protein polypeptide chains to find structural similarities.

Related Experiment Videos

  • CE generates structure alignments, sequence alignments, and Cartesian coordinates for aligned structures.
  • Comparisons can be performed on the entire Protein Data Bank (PDB) or subsets, with user-uploaded proteins also supported.

    • Main Results:

    • The CE algorithm successfully identifies structurally similar proteins, revealing potential functional links.
    • CE provides alignments and coordinates, enabling detailed analysis via the Compare3D Java applet or local downloads.
    • The CE database serves as a valuable resource for protein structure annotation.

    Conclusions:

    • CE-based structure-structure comparisons are essential for inferring biological function, especially in the context of structural genomics.
    • The CE database and associated tools facilitate the functional annotation of proteins.
    • This approach complements traditional sequence-based methods for uncovering protein relationships.