Flexible docking of ligands into synthetic receptors using a two-sided incremental construction algorithm.

We present a new algorithm for the fast and reliable structure prediction of synthetic receptor-ligand complexes. Our method is based on the protein-ligand docking program FlexX and extends our recently introduced docking technique for synthetic receptors, which has been implemented in the program FlexR. To handle the flexibility of the relevant molecules, we apply a novel docking strategy that uses an adaptive two-sided incremental construction algorithm which incorporates the structural flexibility of both the ligand and synthetic receptor. We follow an adaptive strategy, in which one molecule is expanded by attaching its next fragment in all possible torsion angles, whereas the other (partially assembled) molecule serves as a rigid binding partner. Then the roles of the molecules are exchanged. Geometric filters are used to discard partial conformations that cannot realize a targeted interaction pattern derived in a graph-based precomputation phase. The process is repeated until the entire complex is built up. Our algorithm produces promising results on a test data set comprising 10 complexes of synthetic receptors and ligands. The method generated near-native solutions compared to crystal structures in all but one case. It is able to generate solutions within a couple of minutes and has the potential of being used as a virtual screening tool for searching for suitable guest molecules for a given synthetic receptor in large databases of guests and vice versa.