3D-partner -- a web server to infer interacting partners and binding models
What you can do:
Predict interacting partners and binding models.
Highlights:
- 3D-partner first utilizes IMPALA to identify homologous structures (templates) of a query from a heterodimer profile library.
- The interacting-partner sequence profiles of these templates are then used to search interacting candidates of the query from protein sequence databases (e.g. SwissProt) by PSI-BLAST.
- We developed a new scoring function, which includes the contact-residue interacting score (e.g. the steric, hydrogen bonds, and electrostatic interactions) and the template consensus score (e.g. couple-conserved residue and the template similarity scores), to evaluate how well the interfaces between the query and interacting candidates.
- Based on this scoring function, 3D-partner provides the statistic significance, the binding models (e.g. hydrogen bonds and conserved amino acids) and functional annotations of interacting partners.
- The correlation between experimental energies and predicted binding affinities of our scoring function is 0.91 on 275 mutated residues from the ASEdb.
- The average precision of the server is 0.72 on 563 queries and the execution time of this server for a query is approximately 15 s on average.
- These results suggest that the 3D-partner server can be useful in protein-protein interaction predictions and binding model visualizations.
Keywords:
- Binding Sites
- Gene Expression Profiling
- Protein Binding
- Protein Interaction Mapping
- Protein Structure
- interacting partners
- binding models
Literature & Tutorials:
This record last updated: 06-02-2008