Detecting near-native docking decoys by Monte Carlo stability analysis.

Genome informatics. International Conference on Genome Informatics

PubMedID: 18546488

Lorenzen S. Detecting near-native docking decoys by Monte Carlo stability analysis. Genome Inform. 2008;18206-14.
Since protein complex crystallization is expensive and time-consuming, computational docking tools provide a valuable method to investigate protein interactions. While the sampling of possible docked conformers of two proteins can be performed efficiently by Fast Fourier Transform (FFT) methods, the selection of near-native decoys from the pool of thousands of possible decoys is still far from being solved. Here, a new approach for docking decoy selection by Monte Carlo stability analysis is presented. In the course of replica exchange Monte Carlo simulations (REMC), replica from near-native decoys show a significantly lower structural diversity than replica from non-native decoys. The effect is successfully applied to rank docking decoys in a benchmark set of 59 protein complexes.