Optimised amino acid specific weighting factors for unbound protein docking

BackgroundOne 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.ResultsFor 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.ConclusionUse of the optimised amino acid specific parameters yields a strong increase of near-native structures on the first ranks of the prediction.

• Publication year

  2006

• Venue

  BMC Bioinformatics

• Publication date

  2006-07-14

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-7-344PMID 16842615PMCID 1534072
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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