A new protein-protein docking scoring function based on interface residue properties

Motivation: Protein–protein complexes are known to play key roles in many cellular processes. However, they are often not accessible to experimental study because of their low stability and difficulty to produce the proteins and assemble them in native conformation. Thus, docking algorithms have been developed to provide an in silico approach of the problem. A protein–protein docking procedure traditionally consists of two successive tasks: a search algorithm generates a large number of candidate solutions, and then a scoring function is used to rank them. Results: To address the second step, we developed a scoring function based on a Voronoı¨ tessellation of the protein threedimensional structure. We showed that the Voronoı¨ representation may be used to describe in a simplified but useful manner, the geometric and physico-chemical complementarities of two molecular surfaces. We measured a set of parameters on native protein–protein complexes and on decoys, and used them as...

• Type: Journal
• Year: 2007
• Where: BIOINFORMATICS
• Authors: Julie Bernauer, Jérôme Azé, Joël Janin, Anne Poupon
• Keywords: Algorithms, BIOINFORMATICS 2007, Protein–protein Complexes, Scoring Function