About the Research
Generation of novel reactions by means of reccurent neural networks
I graduated from the Institute of Chemistry, Department of Organoelement and Polymer Chemistry (Kazan, Russia) in 2009. My diploma work was devoted to the synthesis of organophosphorus compounds and study of their polyhedral complexes with copper. Then, I was employed at the same lab as synthetic chemist. In 2012, I entered to Double-Diploma Master Program in Chemoinformatics between Kazan Federal University and University of Strasbourg. My master thesis was devoted to profiling of biological activities for molecules with Generative Topographic Mapping approach. My PhD project at the University of Strasbourg concerned development of predictive models for kinetic and theromynamic properties of reactions using the Condensed Graph of Reaction approach. Then I worked in Kazan Federal University on reaction data analysis, structure-reactivity modeling and computer-aided synthesis design, and participated in other projects related to in silico drug design and predictive modeling of material properties. Now I am working at ICReDD, Hokkaido University, Japan on generation of novel reactions by means of Recurrent Neural Networks and development of database for fast storage and search of chemical data.
Representative Research Achievements
- Sydnone-alkyne cycloaddition: Which factors are responsible for reaction rate ?
T.R. Gimadiev, O. Klimchuk, R.I. Nugmanov, T.I. Madzhidov, A. Varnek , J. Mol. Struct., 2019, 1198
- CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing
R.I. Nugmanov, R.N. Mukhametgaleev, T. Akhmetshin, T.R. Gimadiev, V.A. Afonina, T.I. Madzhidov, A. Varnek , JCIM, 2019, 59, 2516–2521
- Bimolecular Nucleophilic Substitution Reactions: Predictive Models for Rate Constants and Molecular Reaction Pairs Analysis
T. Gimadiev, T. Madzhidov, I. Tetko, R. Nugmanov, I. Casciuc, O. Klimchuk, A. Bodrov, P. Polishchuk, I. Antipin, A. Varnek , Mol. Inf., 2019, 38
- Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules
D.V. Zankov, T.I. Madzhidov, A. Rakhimbekova, T.R. Gimadiev, R.I. Nugmanov, M.A. Kazymova, I.I. Baskin, A. Varnek , JCIM., 2019
- Assessment of tautomer distribution using the condensed reaction graph approach
T.R. Gimadiev, T.I. Madzhidov, R.I. Nugmanov, I.I. Baskin, I.S. Antipin, A. Varnek, JCAMD., 2018, 32, 401–414
- Structure–reactivity modeling using mixture-based representation of chemical reactions
P. Polishchuk, T. Madzhidov, T. Gimadiev, A. Bodrov, R. Nugmanov, A. Varnek, JCAMD., 2017, 31, 829–839