RDOCK: Refinement of rigid-body protein docking predictions

RDOCK: refinement of rigid-body protein docking predictions.

We present a simple and effective algorithm RDOCK for refining unbound predictions generated by a rigid-body docking algorithm ZDOCK, which has been developed earlier by our group. The main component of RDOCK is a three-stage energy minimization scheme, followed by the evaluation of electrostatic and desolvation energies. Ionic side chains are kept neutral in the first two stages of minimizatio...

Improving CAPRI predictions: optimized desolvation for rigid-body docking.

The ICM Docking and Interface Side-Chain Optimization (ICM-DISCO) showed promising predictive results during the first CAPRI experiment by successfully finding medium- or high-accuracy models in 3 of the 7 targets. A key factor was the ability to recognize near-native rigid-body geometries in a relatively low number of alternative docking poses, together with the successful refinement of the ri...

Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization.

Structures of hitherto unknown protein complexes can be predicted by docking the solved protein monomers. Here, we present a method to refine initial docking estimates of protein complex structures by a Monte Carlo approach including rigid-body moves and side-chain optimization. The energy function used is comprised of van der Waals, Coulomb, and atomic contact energy terms. During the simulati...

Rigid body refinement (basics)

Scoring docked conformations generated by rigid-body protein-protein docking.

Rigid-body methods, particularly Fourier correlation techniques, are very efficient for docking bound (co-crystallized) protein conformations using measures of surface complementarity as the target function. However, when docking unbound (separately crystallized) conformations, the method generally yields hundreds of false positive structures with good scores but high root mean square deviation...