Evaluation of Docking Target Functions by the Comprehensive Investigation of Protein-Ligand Energy Minima.

ABSTRACT: The adequate choice of the docking target function impacts the accuracy of the ligand positioning as well as the accuracy of the protein-ligand binding energy calculation. To evaluate a docking target function we compared positions of its minima with the experimentally known pose of the ligand in the protein active site. We evaluated five docking target functions based on either the MMFF94 force field or the PM7 quantum-chemical method with or without implicit solvent models: PCM, COSMO, and SGB. Each function was tested on the same set of 16 protein-ligand complexes. For exhaustive low-energy minima search the novel MPI parallelized docking program FLM and large supercomputer resources were used. Protein-ligand binding energies calculated using low-energy minima were compared with experim

SUBMITTER: Oferkin IV 

PROVIDER: S-EPMC4674582 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature