Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Research article

Optimised amino acid specific weighting factors for unbound protein docking

Philipp Heuser and Dietmar Schomburg*

Author Affiliations

Cologne University Bioinformatics Center (CUBIC), University of Cologne, Zuelpicher Str. 47, 50674 Koeln, Germany

For all author emails, please log on.

BMC Bioinformatics 2006, 7:344  doi:10.1186/1471-2105-7-344

Published: 14 July 2006

Abstract

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 near-native structures on the first ranks of the prediction.