These are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information. For more information, please see our FAQs.
7 files

G-RMSD: Root Mean Square Deviation Based Method for Three-dimensional Molecular Similarity Determination

submitted on 04.03.2020, 16:45 and posted on 05.03.2020, 11:50 by Tomonori Fukutani,, kohei Miyazawa, Satoru Iwata, Hiroko Satoh
We present the Generalized Root Mean Square Deviation (G-RMSD) method. G-RMSD is an optimization method to calculate the minimal RMSD value of two atomic structures by optimal superimposition. The method is not restricted to systems with an equal number of atoms or a unique atom matching and can handle any type of chemical structure, including transition states and non-valence bond structures. It requires only Cartesian coordinates for the structures, but can also include further information, i.e. atom and bond types. Applications of G-RMSD to the classification of alpha-D-glucose conformers and 3D partial structure search using a dataset containing equilibrium (EQ), dissociation channel (DC), and transition state (TS) structures are demonstrated. We find that G-RMSD allows for a successful classification and mapping for a wide variety of molecular structures.


Tokyo University

Research Organization of Information and Systems

University of Zurich


Email Address of Submitting Author


University of Zurich



ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict interest

Version Notes

First submission