DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
By Eric W. Bell, Yang Zhang. Journal of Cheminformatics, 2019
406 citations recorded by the source corpus.
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 a graph isomorphism searching problem, in which the optimal atomic mapping and RMSD calculation are performed by an exhaustive and fast matching search of all isomorphisms of the ligand structure graph. We show through evaluation of docking poses generated by AutoDock Vina on the CSAR Hi-Q set that DockRMSD is capable of deterministically identifying the minimum symmetry-corrected RMSD and is able to do so without significant loss of computational efficiency compared to other methods. The open-source DockRMSD program can be conveniently integrated with various docking pipelines to assist with accurate atomic mapping and RMSD calculations, which can therefore help improve docking performance, especially for ligand molecules with complicated structural symmetry.
Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry
View Paper: https://www.semanticscholar.org/paper/d8bb0a5c3702a4313062c0d21a12c6304994ec53
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
Citations in the corpus
- RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints (2023, background): “…of the model with the experimentally determined structure shows that for the aligned RNA structures the RMSD of the ligand was as low as 0.956 Å. 30 The analysis of non-covalent interactions with fingeRNAt 21 indicates that almost all contacts between ligand and RNA present in the reference…”