Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses

Local Interaction Density (LID), a Fast and Efficient Tool to Prioritize Docking Poses

Blog Article

Ligand docking at a protein site can be improved by prioritizing poses by similarity to validated binding modes found in the crystal structures of ligand/protein complexes.The interactions formed in the predicted model are searched in each of the reference 3D structures, taken individually.We propose to merge the information provided by all references, creating a single representation of all known binding modes.

The method is called LID, an acronym for Local Interaction Density.LID was benchmarked in apunisw2 a pose prediction exercise on 19 proteins and 1382 ligands using PLANTS as docking software.It was also tested in a virtual screening challenge on eight proteins, with a dataset of 140,000 compounds from DUD-E and PubChem.

LID significantly improved the performance of the docking program in both pose prediction and virtual screening.The gain is comparable to that obtained with a click here rescoring approach based on the individual comparison of reference binding modes (the GRIM method).Importantly, LID is effective with a small number of references.

LID calculation time is negligible compared to the docking time.