DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism.

ABSTRACT: Comparison of ligand poses generated by protein-ligand docking programs has often been carried out with the assumption of direct atomic correspondence between ligand structures. However, this correspondence is not necessarily chemically relevant for symmetric molecules and can lead to an artificial inflation of ligand pose distance metrics, particularly those that depend on receptor superposition (rather than ligand superposition), such as docking root mean square deviation (RMSD). Several of the commonly-used RMSD calculation algorithms that correct for molecular symmetry do not take into account the bonding structure of molecules and can therefore result in non-physical atomic mapping. Here, we present DockRMSD, a docking pose distance calculator that converts the symmetry correction to

SUBMITTER: Bell EW 

PROVIDER: S-EPMC6556049 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature