Detecting near-native docking decoys by Monte Carlo stability analysis.
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.
Lorenzen
Stephan
S
Free University Berlin, Takustr. 6, 14195 Berlin, Germany. lorenzen@chemie.fu-berlin.de
D001665:Binding Sites; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
D011506:Proteins