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Gimadiev et al - RePathDB.pdf (795.53 kB)

Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data

preprint
submitted on 23.10.2020, 01:31 and posted on 23.10.2020, 09:42 by Timur Gimadiev, Ramil Nugmanov, Dinar Batyrshin, Timur Madzhidov, Satoshi Maeda, Pavel Sidorov, Alexandre Varnek
Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph.

History

Email Address of Submitting Author

pavel.sidorov@icredd.hokudai.ac.jp

Institution

ICReDD, Hokkaido University

Country

Japan

ORCID For Submitting Author

0000-0001-6462-702X

Declaration of Conflict of Interest

No conflict of interest

Exports