Protein-protein docking with a reduced protein model accounting for side-chain flexibility.

ABSTRACT: A protein-protein docking approach has been developed based on a reduced protein representation with up to three pseudo atoms per amino acid residue. Docking is performed by energy minimization in rotational and translational degrees of freedom. The reduced protein representation allows an efficient search for docking minima on the protein surfaces within. During docking, an effective energy function between pseudo atoms has been used based on amino acid size and physico-chemical character. Energy minimization of protein test complexes in the reduced representation results in geometries close to experiment with backbone root mean square deviations (RMSDs) of approximately 1 to 3 A for the mobile protein partner from the experimental geometry. For most test cases, the energy-minimized exper

SUBMITTER: Zacharias M 

PROVIDER: S-EPMC2323887 | biostudies-literature | 2003 Jun

REPOSITORIES: biostudies-literature