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SURFACE: a database of protein surface regions for functional annotation.
Fabrizio Ferrè1, Gabriele Ausiello, Andreas Zanzoni
1Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy.
Nucleic Acids Research
|December 19, 2003
Summary
The SURFACE database annotates and compares protein surface regions, revealing functional sites. This method highlights similarities missed by other comparisons, aiding in protein function discovery.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein surface regions are crucial for function and interactions.
- Existing methods for comparing protein surfaces have limitations.
Purpose of the Study:
- To introduce the SURFACE database, a resource for annotated and compared protein surface regions.
- To develop and apply a novel method for local structural comparison of protein surfaces.
Main Methods:
- A non-redundant set of protein chains was used to create a database of protein surface patches.
- Patches were annotated with sequence and structure-derived information.
- An all-versus-all comparison of surface patches was performed using a new structural comparison procedure.
Main Results:
- The SURFACE database provides annotated protein surface patches, defined as putative functional sites.
- A similarity score derived from stringent comparison parameters enables reliable annotation by similarity.
- This approach identifies similarities not detectable by traditional sequence or structure comparison methods.
Conclusions:
- The SURFACE database offers a valuable resource for understanding protein function and interactions.
- Annotation by similarity of surface regions is a powerful tool for protein analysis.
- The web interface provides visualization of surface patches, annotations, and structural superpositions.