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  • Title: Optimised amino acid specific weighting factors for unbound protein docking.
    Author: Heuser P, Schomburg D.
    Journal: BMC Bioinformatics; 2006 Jul 14; 7():344. PubMed ID: 16842615.
    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.
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