A fragment-based scoring function to re-rank ATP docking results

ATP is involved in numerous biochemical reactions in living cells interacting with different proteins. Molecular docking simulations provide considerable insight into the problem of molecular recognition of this substrate. To improve the selection of correct ATP poses among those generated by docking algorithms we propose a post-docking re-ranking criterion. The method is based on detailed analysis of the intermolecular interactions in 50 high-resolution 3D-structures of ATP-protein complexes. A distinctive new feature of the proposed method is that the ligand molecule is divided into fragments that differ in their physical properties. The placement of each of them into the binding site is judged separately by different criteria, thus avoiding undesirable averaging of the scoring function terms by highlighting those relevant for particular fragments. The scoring performance of the new criteria was tested with the docking solutions for ATP-protein complexes and a significant improvement in the selection of correct docking poses was observed, as compared to the standard scoring function.