Sampling Geometries of Protein-Protein Complexes

Aysam Guerler (
Stephan Lorenzen (
Floran Krull (
Ernst-Walter Knapp (

Frie Universit├Ąt Berlin, Department of Chemistry and Biochemistry, Fabeckstr. 36a, 14195, Berlin-Dahlem, Germany


Protein-protein docking is a major task in structural biology. In general, the geometries of protein pairs are sampled by generating docked conformations, analyzing them with scoring functions and selecting appropriate geometries for further refinement. Here, we present an algorithm in real space to sample geometries of protein pairs. Therefore, we initially determine uniformly distributed points on the surfaces of the two protein structures to be docked and additionally define a set of uniformly distributed rotations. Then, the sampling method generates structures of protein pairs as follows: (i) We rotate one protein of the protein pair according to a selected rotation and (ii) translate it along a line connecting two surface points belonging to different proteins such that these surface points coincide. The resulting protein pair geometries are then analyzed and selected using a scoring function that considers residues and atom pairs. We applied this approach to a set of 22 enzymeinhibitor complexes and demonstrate that a discretisation of the rigid-body search in real space provides an efficient and robust sampling scheme. Our method generates decoy sets with a considerable fraction of near-native geometries for all considered enzyme-inhibitor complexes.

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Japanese Society for Bioinformatics