ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation.

We propose a simple but efficient and accurate method to generate protein-ligand complex structures, called Concentrated ligand Docking (ColDock). This method consists of multiple independent molecular dynamics simulations in which ligands are initially distributed randomly around a protein at relatively high concentration (∼100 mM). This condition significantly increases the probability of the ligand exploring the protein surface, which induces spontaneous ligand binding to the correct binding sites within a 100 ns MD. After clustering of the protein-bound ligand poses, representatives of the populationally dominant clusters are considered as predicted ligand poses. We applied ColDock to four cases starting from holo protein structures and showed that ColDock can generate "correct" ligand poses very similar to the crystal complex structures. Correct ligand poses are also well reproduced in three out of four cases started from apo structures, with the exception being a case with an initially closed binding pocket. The results indicate that ColDock can be used as a protein-ligand docking as long as the ligand binding pocket is initially open. Plausible protein-ligand complex structures can be easily generated by conducting the ColDock procedure using standard MD simulation software.