GlamDock: development and validation of a new docking tool on several thousand protein-ligand complexes

In this study, we present GlamDock, a new docking tool for flexible ligand docking. GlamDock (version 1.0) is based on a simple Monte Carlo with minimization procedure. The main features of the method are the energy function, which is a continuously differentiable empirical potential, and the definition of the search space, which combines internal coordinates for the conformation of the ligand, with a mapping-based description of the rigid body translation and rotation. First, we validate GlamDock on a standard benchmark, a set of 100 protein-ligand complexes, which allows comparative evaluation to existing docking tools. The results on this benchmark show that GlamDock is at least comparable in efficiency and accuracy to the best existing docking tools. The main focus of this work is the validation on the scPDB database of protein-ligand complexes. The size of this data set allows a thorough analysis of the dependencies of docking accuracy on features of the protein-ligand system. In particular, it allows a two-dimensional analysis of the results, which identifies a number of interesting dependencies that are generally lost or even misinterpreted in the one-dimensional approach. The overall result that GlamDock correctly predicts the complex structure in practically half of the cases in the scPDB is important not only for screening ligands against a particular protein but even more so for inverse screening, that is, the identification of the correct targets for a particular ligand.