Optimised amino acid specific weighting factors for unbound protein docking

Background: One of the most challenging aspects of protein-protein docking is the inclusion of flexibility into the docking procedure. We developed a postfilter where the grid-representation of proteins for docking is extended by an optimised weighting factor for each amino acid. Results: For up to 86% of the evaluated complexes a near-native structure was within the top 5% of the ranked prediction output. The weighting factors obtained by the optimisation procedure correlate to a certain extent with the flexibility of the amino acids, their hydrophobicity and with their propensity to be in the interface. Conclusion: Use of the optimised amino acid specific parameters yields a strong increase of nearnative structures on the first ranks of the prediction. Background Protein-protein interactions and complex formation play a central role in a broad range of biological processes, including hormone-receptor binding, protease inhibition, antibody-antigen interaction and signal transduction ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Philipp Heuser, Dietmar Schomburg
• Keywords: Amino Acid, BMCBI 2006, Protein-protein Interactions, Proteins