研究紹介
研究テーマ
Generation of novel reactions by means of reccurent neural networks
キーワード
研究概要
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.
代表的な研究成果
- 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
DOI: 10.1016/j.molstruc.2019.126897 - 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
DOI: 10.1021/acs.jcim.9b00102 - 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
DOI: 10.1002/minf.201800104 - 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
DOI: 10.1021/acs.jcim.9b00722 - 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
DOI: 10.1007/s10822-018-0101-6 - 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
DOI: 10.1007/s10822-017-0044-3
関連する研究記事
業績一覧
2023年
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Predicting Highly Enantioselective Catalysts Using Tunable Fragment Descriptors
, P. Sidorov, C. D. Zhu, Y. Nagata, T. Gimadiev, A. Varnek, B. List, Angew. Chem., Int. Ed., 2023, ,
DOI: 10.1002/anie.202218659
2022年
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CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data
, R. Nugmanov, A. Khakimova, A. Fatykhova, T. Madzhidov, P. Sidorov, A. Varnek, J. Chem. Inf. Model., 2022, 62, 2015-2020
DOI: 10.1021/acs.jcim.1c01105
2021年
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Machine Learning Modelling of Chemical Reaction Characteristics: Yesterday, Today, Tomorrow
, A. Rakhimbekova, V. A. Afonina, T. R. Gimadiev, R. N. Mukhametgaleev, R. I. Nugmanov, I. Baskinc, A. Varnekkd, Mendeleev Communications, 2021, 31, 769-780
DOI: 10.1016/j.mencom.2021.11.003
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Atom-to-Atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies
, N. Dyubankova, T. I. Madzhidov, R. I. Nugmanov, J. Verhoeven, T. R. Gimadiev, V. A. Afonina, Z. Ibragimova, A. Rakhimbekova, P. Sidorov, A. Gedich, R. Suleymanov, R. Mukhametgaleev, J. Wegner, H. Ceulemans, A. Varnek, Molecular Informatics, 2021, 41,
DOI: 10.1002/minf.202100138
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Discovery of Novel Chemical Reactions by Deep Generative Recurrent Neural Network
, I. Baskin, T. Gimadiev, A. Mukanov, R. Nugmanov, P. Sidorov, G. Marcou, D. Horvath, O. Klimchuk, T. Madzhidov, A. Varnek, Scientific Reports, 2021, 11, 15
DOI: 10.1038/s41598-021-81889-y
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Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data
, R. Nugmanov, D. Batyrshin, T. Madzhidov, S. Maeda, P. Sidorov, A. Varnek, J. Chem. Inf. Model., 2021, 61, 554-559
DOI: 10.1021/acs.jcim.0c01280
2019年
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Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules
, TI. Madzhidov, A. Rakhimbekova, TR. Gimadiev, RI. Nugmanov, MA. Kazymova, II. Baskin, A. Varnek, J. Chem. Inf. Model., 2019, 59, 4569-4576
DOI: 10.1021/acs.jcim.9b00722