Docking protein domains in contact space

Background: Many biological processes involve the physical interaction between protein domains. Understanding these functional associations requires knowledge of the molecular structure. Experimental investigations though present considerable difficulties and there is therefore a need for accurate and reliable computational methods. In this paper we present a novel method that seeks to dock protein domains using a contact map representation. Rather than providing a full three dimensional model of the complex, the method predicts contacting residues across the interface. We use a scoring function that combines structural, physicochemical and evolutionary information, where each potential residue contact is assigned a value according to the scoring function and the hypothesis is that the real configuration of contacts is the one that maximizes the score. The search is performed with a simulated annealing algorithm directly in contact space. Results: We have tested the method on interact...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Stefano Lise, Alice Walker-Taylor, David T. Jones
• Keywords: BMCBI 2006, Physical Interactions, Proteins, Scoring Function