Optimised amino acid specific weighting factors for unbound protein docking

• Main Authors: Schomburg Dietmar, Heuser Philipp
• Format: Article
• Language: English
• Published: BMC 2006-07-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/7/344

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>Use of the optimised amino acid specific parameters yields a strong increase of near-native structures on the first ranks of the prediction.</p>