Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets

Background: In structural genomics, an important goal is the detection and classification of protein–protein interactions, given the structures of the interacting partners. We have developed empirical energy functions to identify native structures of protein–protein complexes among sets of decoy structures. To understand the role of amino acid diversity, we parameterized a series of functions, using a hierarchy of amino acid alphabets of increasing complexity, with 2, 3, 4, 6, and 20 amino acid groups. Compared to previous work, we used the simplest possible functional form, with residue–residue interactions and a stepwise distance-dependence. We used increased computational ressources, however, constructing 290,000 decoys for 219 protein–protein complexes, with a realistic docking protocol where the protein partners are flexible and interact through a molecular mechanics energy function. The energy parameters were optimized to correctly assign as many native complexes as poss...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Guillaume Launay, Raul Mendez, Shoshana J. Wodak, Thomas Simonson
• Keywords: Amino Acid, BMCBI 2007, Decoy Structures, Energy Function