Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock.

ABSTRACT:

Background

Molecular docking methods are commonly used for predicting binding modes and energies of ligands to proteins. For accurate complex geometry and binding energy estimation, an appropriate method for calculating partial charges is essential. AutoDockTools software, the interface for preparing input files for one of the most widely used docking programs AutoDock 4, utilizes the Gasteiger partial charge calculation method for both protein and ligand charge calculation. However, it has already been shown that more accurate partial charge calculation - and as a consequence, more accurate docking- can be achieved by using quantum chemical methods. For docking calculations quantum chemical partial charge calculation as a routine was only used for ligands so far. The newly develop

SUBMITTER: Bikadi Z 

PROVIDER: S-EPMC2820493 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature