Combination of scoring schemes for protein docking

Background: Docking algorithms are developed to predict in which orientation two proteins are likely to bind under natural conditions. The currently used methods usually consist of a sampling step followed by a scoring step. We developed a weighted geometric correlation based on optimised atom specific weighting factors and combined them with our previously published amino acid specific scoring and with a comprehensive SVM-based scoring function. Results: The scoring with the atom specific weighting factors yields better results than the amino acid specific scoring. In combination with SVM-based scoring functions the percentage of complexes for which a near native structure can be predicted within the top 100 ranks increased from 14% with the geometric scoring to 54% with the combination of all scoring functions. Especially for the enzyme-inhibitor complexes the results of the ranking are excellent. For half of these complexes a near-native structure can be predicted within the first ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Philipp Heuser, Dietmar Schomburg
• Keywords: Acid Specific Scoring, BMCBI 2007, Scoring Functions, Svm-based Scoring Functions