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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.

Optimised amino acid specific weighting factors for unbound protein docking