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PeptiSite: a structural database of peptide binding sites in 4D
Chayan Acharya1, Irina Kufareva1, Andrey V Ilatovskiy2
1UCSD, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
Biochemical and Biophysical Research Communications
|January 11, 2014
Summary
PeptiSite is a new database detailing peptide-binding sites. It uses a unique ensemble representation to capture the dynamic nature of these interactions, aiding in understanding protein-peptide binding.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Chemistry
Background:
- Understanding protein-peptide interactions is crucial for drug discovery and molecular biology.
- Existing databases often lack comprehensive structural and dynamic characterization of binding sites.
Purpose of the Study:
- To create a comprehensive database of peptide-binding sites.
- To provide a novel representation of binding sites that captures their dynamic nature.
- To facilitate the study of structural principles governing protein-peptide interactions.
Main Methods:
- Development of the PeptiSite database.
- Ensemble representation of peptide-binding sites.
- Characterization of binding site architecture, including multimeric assemblies, cofactors, and metal ions.
- Analysis of consensus interaction motifs and conserved determinants.
Main Results:
- The database currently contains 585 proteins with 650 characterized peptide-binding sites.
- PeptiSite introduces a unique ensemble site representation, adding a fourth dimension to structural data.
- Comprehensive characterization of binding site architecture and identification of conserved interaction determinants are included.
Conclusions:
- PeptiSite offers a valuable resource for understanding the structural basis of protein-peptide interactions.
- The database can aid in the development of efficient peptide docking benchmarks.
- Interactive visualization tools are available through the ActiveICM web-browser plugin.
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