Detecting Near-Native Docking Decoys by Monte Carlo Stability Analysis

Stephan Lorenzen (lorenzen@chemie.fu-berlin.de)

Macromolecular Modelling Group, Free University Berlin, Takustr. 6, 14195 Berlin, Germany


Abstract

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.

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Japanese Society for Bioinformatics