title: Optimised amino acid specific weighting factors for unbound protein docking.
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.
  
  
  CONCLUSIONS
  Use of the optimised amino acid specific parameters yields a strong increase of near-native structures on the first ranks of the prediction.
authors.affiliation: Cologne University Bioinformatics Center, University of Cologne, Zuelpicher Str, 47, 50674 Koeln, Germany. philipp.heuser@uni-koeln.de
authors.forename: Philipp
authors.initials: P
authors.lastname: Heuser
authors.forename: Dietmar
authors.initials: D
authors.lastname: Schomburg
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D000596:Amino Acids; D011506:Proteins