• Timur Gimadiev, Ramil Nugmanov, Aigul Khakimova, Adeliya Fatykhova, Timur Madzhidov, Pavel Sidorov, Alexandre Varnek (2021). CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data. Journal of Chemical Information and Modeling.
• Timur Gimadiev, Ramil Nugmanov, Aigul Khakimova, Adeliya Fatykhova, Timur Madzhidov, Pavel Sidorov, Alexandre Varnek (2021). CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.1c01105

• Fatykhova A.A., Nougmanov R.I., Mukhametgaleev R.N., Madzhidov T.I. , Varnek A. Prediction of synthesis path of chemical compound and its analogues. XII International Conference on Chemistry for Young Scientists "Mendeleev 2021" - Book of Abstracts (St Petersburg, September 06-10, 2021). - St Petersburg, 2021. - P. 125. (ISBN 978-5-9651-1364-4).
• Rakhimbekova, A. Cross-validation strategies in QSPR modelling of chemical reactions / A. Rakhimbekova, T.N. Akhmetshin, G.I. Minibaeva, R.I. Nugmanov, T.R. Gimadiev, T.I. Madzhidov, I.I. Baskin, A. Varnek // SAR and QSAR in Environmental Research -2021.-32(3)-pp.207-219. doi: 10.1080/1062936X.2021.1883107.

• Rakhimbekova, A. Comprehensive analysis of applicability domains of QSPR models for chemical reactions / A. Rakhimbekova, T.I. Madzhidov, R.I. Nugmanov, T.R. Gimadiev, I.I. Baskin, A. Varnek // Int. J. Mol. Sci.-2020.-21(15)-pp.1-20. doi: 10.3390/ijms21155542.
• Фатыхова А.А. Предсказание пути синтеза целевого соединения и его аналогов на основе алгоритма обучения с подкреплением / А.А. Фатыхова, Т.И. Маджидов, В.А. Малых, И.С. Кузнецов, Б.И. Пякилля, Р.И. Нугманов, А. Варнек // Сборник тезисов докладов Шестой Междисциплинарной конференции «Молекулярные и Биологические аспекты Химии, Фармацевтики и Фармакологии« / под редакцией К.В. Кудрявцева и Е.М. Паниной. - М.: «Перо«, 2020. - С. 108
• Madzhidov T.I. Deep conditional variational autoencoder for reaction conditions prediction / T.I.Madzhidov, D.A. Mazitov, V.A. Afonina, T.N. Akhmetshin, J.D. Skibina, A.I. Lin, R.I. Nugmanov, A. Varnek // 3rd RSC-BMCS/RSC-CICAG Artificial Intelligence in Chemistry. - London, 2020. - P. 55.
  thesis.pdf

• Rakhimbekova A. Search of optimal approaches for defining applicability domain of models for predicting properties of chemical reactions/ Rakhimbekova A., Nugmanov R.I., Gimadiev T.R., Madzhidov T.I., Varnek A. // Book of abstracts Markovnikov Congress on Organic Chemistry 21-28 June 2019, Moscow-Kazan, Russia. - 2019. - P. 187
• Zankov D.V, Madzhidov T.I, Rakhimbekova A, Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules//Journal of Chemical Information and Modeling. - 2019. - Vol. 59, Is. 11. - 4569-4576
• Zankov D.V. Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules/ Zankov D.V, Madzhidov T.I, Rakhimbekova A, Gimadiev T.R., Nugmanov R.I., Kazymova M.A., Baskin I.I., Varnek A.//Journal of Chemical Information and Modeling. - 2019. - Vol. 59, Is. 11. - pp. 4569-4576.
• Введение в хемоинформатику: учеб. пособие. Ч. 6. Химическое пространство и виртуальный скрининг / Т.И. Маджидов, И.И. Баскин, А.А. Варнек. – Казань: Изд-во Казан. ун-та, 2019. – 240 с.
• Fatykhova A. CGR-DB cartridge in chemical synthesis planning / A. Fatykhova, R. Nugmanov, T. Madzhidov, A. Varnek // Markovnikov Congress on Organic Chemistry (June 201-28): book of abstracts, 2019. - P 147.
  F_mc150cgrdb.pdf
• Gimadiev T.R, Klimchuk O, Nugmanov R.I, Sydnone-alkyne cycloaddition: Which factors are responsible for reaction rate ?//Journal of Molecular Structure. - 2019. - Vol.1198 - Art. № 126897.

• Assessment of tautomer distribution using the condensed reaction graph approach / T. Gimadiev, T. Madzhidov, R. Nugmanov, I.I. Baskin, I.S. Antipin, A. Varnek // Journal of Computer-Aided Molecular Design.? 2018.? P.1-14
• Gimadiev T.R, Madzhidov T.I, Nugmanov R.I, Assessment of tautomer distribution using the condensed reaction graph approach//Journal of Computer-Aided Molecular Design. - 2018. - Vol.32, Is.3. - P.401-414.
• Afonina, V.A. Reaction conditions prediction by artificial neural networks / V.A. Afonina, A. Delova, R.I. Nugmanov, T.I. Madzhidov, O. Klimchuk, A. Varnek // Third International School-Seminar «From Empirical to Predictive Chemistry« (Kazan, 5-7 April 2018): book of abstracts. - Kazan: Kazan Federal University, 2018. - P. 31.
• Fatykhova A. Automated system for searching reactions, reaction centers and analysis of protective groups using CGR-DB cartridge / A. Fatykhova, R. Nugmanov, R. Mukhametgaleev, S. Musaeva, V. Afonina, T. Madzhidov, A. Varnek //In search of models for personalized medicine. Abstracts volume of V International conference “POSTGENOME'2018” (October 29 - November 2, 2018) - Kazan: KFU publishing office. 2018. - P. 319. (poster presentation)
  abstract.pdf
• Fatykhova A. On-line reaction database cartridge with built-in condensed graph of reaction-based search engine / A. Fatykhova, R. Nugmanov, T. Madzhidov, A. Varnek // Third International School-Seminar «From Empirical to Predictive Chemistry« (April 5–7, 2018, Kazan, Russia): book of abstracts / ed.: T.I. Madzhidov, V.A. Afonina; I.S. Antipin. Kazan: Kazan University Press, 2018. – 96 p.
  ONLINE_REACTION_DATABASE_CARTRIDGE.pdf
• Nugmanov R. On-Line Reaction Database Cartridge with Built-in Condensed Graph of Reaction-Based Search Engine / R. Nugmanov, A. Fatykhova, T. Madzhidov, A. Varnek // 6th Strasbourg Summer School in Chemoinformatics: Strasbourg, 25 June - 29 June 2018. - Strasbourg, 2018. - P. 62.
  F_P24_Nugmanov.pdf
• Фатыхова А. А. CGR-db — интегрированный картридж для системы управления базой данных химических реакций / А. А. Фатыхова, Р. И. Нугманов, Т. И. Маджидов, А. Варнек // III Международная школа-конференция студентов, аспирантов и молодых ученых «Материалы и технологии XXI века«: 29 - 31 октября 2018. - КФУ, 2018.
• Lin A, Horvath D, Afonina V, Mapping of the Available Chemical Space versus the Chemical Universe of Lead-Like Compounds//ChemMedChem. - 2018. - Vol. 13, Is. 6. - P. 540-554.

• T.I. Madzhidov, T.R. Gimadiev, D.A. Malakhova, R.I. Nugmanov, I.I. Baskin, I.S. Antipin, and .A. Varnek. Structure-Reactivity modeling for Dielas-alder reactions based on the condensed REACTION graph approach.Journal of Structural Chemistry,2017, Vol.58, No 4,p. 685-691
• Structure?reactivity modeling using mixture-based representation of chemical reactions / P. Polishchuk, T. Madzhidov, T. Gimadiev, A. Bodrov, R. Nugmanov, A. Varnek // Journal of Computer-Aided Molecular Design.? 2017.? P.1-11
• Afonina, V.A. Automatic system for prediction of optimal condition for hydrogenation reactions / V. Afonina, A. Lin, T. Madzhidov, R. Nugmanov, I. Antipin, O. Klimchuk, A. Varnek // 3rd Kazan Summer School on Chemoinformatics (5–7 July 2017, Kazan). – Kazan: Kazan Federal University, 2017. - P. 38.
• Nugmanov R. CGR-DB. INTERACTIVE REACTION DATABASE AND CGR-BASED SEARCH ENGINE / R. Nugmanov, B. Sattarov, A. Fatykhova, A. Kutlushina, F. Bekmuratova, Z. Khayrullina, E. Moiseeva, R. Gimatev, T. Madzhidov, A. Varnek // 3rd Kazan Summer School on Chemoinformatics. (5–7 July 2017, Kazan). Books of abstracts. – Kazan: Kazan Federal University, 2017. – 92.
  F_tuzis.pdf
• Polishchuk P, Madzhidov T, Gimadiev T, Structure?reactivity modeling using mixture-based representation of chemical reactions//Journal of Computer-Aided Molecular Design. - 2017. - Vol.31, Is.9. - P.829-839.
• Baskin Igor I., Madzhidov Timur I., Antipin Igor S., Artificial intelligence in synthetic chemistry: achievements and prospects//RUSSIAN CHEMICAL REVIEWS. - 2017. - Vol.86, Is.11. - P.1127-1156.
• Madzhidov, T. Handling of Markush Structures / T.I. Madzhidov, R.I. Nugmanov, A. Varnek //Tutorials in Chemoinformatics. - Hoboken: John Wiley & Sons, 2017 - p. 67-73
• Madzhidov T. I., Gimadiev T. R., Malakhova D. A., STRUCTURE-REACTIVITY RELATIONSHIP IN DIELS-ALDER REACTIONS OBTAINED USING THE CONDENSED REACTION GRAPH APPROACH//JOURNAL OF STRUCTURAL CHEMISTRY. - 2017. - Vol.58, Is.4. - P.650-656.

• Sidorov, P. Visualization and analysis of large dataset of chemical reactions using GTM / P. Sidorov, A. Lin, T. Madzhidov, A. Varnek // 5th Chemoinformatics Strasbourg Summer School: book of abstracts, June 27 - July 1, 2016, Strasbourg, France.
• Afonina V.A. Mapping of the Chemical Uni-verse versus Available Chemical Space of Lead-Like Compounds / V.A. Afonina, D. Horvath, A. Varnek // 5th Chemoinformatics Strasbourg Summer School: Strasbourg, 27 June - 1 July 2016. – P. 77.
• Glavatskikh M. Predictive Models for Halogen-bond Basicity of Binding Sites of Polyfunctional Molecules / M. Glavatskikh, T. Madzhidov, V. Solov'ev, G. Marcou, D. Horvath, J. Graton, J.-Y. Le Questel, A. Varnek // Molecular Informatics. - 2016. - V. 35, Is. 2. - Pp. 70-80.
• Madzhidov, T.I. Asessment of optimal reaction conditions: deprotection in catalytic hydrogenation conditions / T.I. Madzhidov, A.I. Lin, R.I. Nugmanov, O. Klimchuk, I. Antipin, A. Varnek // 5th Chemoinformatics Strasbourg Summer School: book of abstracts, June 27 - July 1, 2016, Strasbourg, France. - P. 52.
• Afonina, V.A. Mapping of the Chemical Universe vs Available Chemical Space of Lead-Like Compounds / V.A. Afonina, D. Horvath, A. Varnek // XX Mendeleev Congress on general and applied chemistry. Five-volumes book. Vol.5: abstracts. - Ekaterinburg: Ural Branch of the Russian Academy of Sciences, 2016. - P.126.
• Klimchuk, O. Assessment of optimal conditions in reactions of catalytic hydrogenation / O. Klimchuk, A.I. Lin, T.I. Madzhidov, R.I. Nugmanov, I. Antipin, A. Varnek // International School-Seminar on Computer-Aided Molecular Design: May 18-20, 2016, Kazan, Russia: Book of Abstracts and Scientific Program. - P. 9.
• Glavatskikh, M. Predictive models for diiodine basicity scale of halogen bond / M. Glavatskikh, T. Madzhidov, V. Solov`ev, D. Horvath, G. Marcou, A. Varnek // International School-Seminar on Computer-Aided Molecular Design: May 18-20, 2016, Kazan, Russia: Book of Abstracts and Scientific Program. - P. 14
• Gimadiev, T.R. Predicting of reactivity for biorthogonal reactions of sydnones heterocycles with alkynes / T.R. Gimadiev, T.I. Madzhidov, R.I. Nugmanov, A. Varnek // International School-Seminar on Computer-Aided Molecular Design: May 18-20, 2016, Kazan, Russia: Book of Abstracts and Scientific Program. - P. 19.
• Nugmanov R.I. Automatic reaction processing and standardization workflow / R.I. Nugmanov, T.I. Madzhidov, A. Varnek // International School-Seminar on Computer-Aided Molecular Design: May 18-20, 2016, Kazan, Russia: Book of Abstracts and Scientific Program. - P. 37.
• Nugmanov, R.I. Workflow for reaction database cleaning and data standartization / R.I. Nugmanov, T.I. Madzhidov, A. Varnek // 5th Chemoinformatics Strasbourg Summer School: book of abstracts, June 27 - July 1, 2016, Strasbourg, France. - P. 54

• Gimadiev T.R. Prediction of Tautomer Equilibrium Constants Using Condensed Graphs of Reaction / T.R. Gimadiev, R. I. Nugmanov, T. I. Madzhidov, I. I. Baskin, I. S. Antipin, A. A. Varnek // Second Kazan Summer School in Chemoinformatics: July 6-9, 2015, Kazan, Russia: Book of Abstracts and Scientific Program. - Kazan, 2015. - P. 34.
• Madzhidov, T.I. Condensed graph of reaction approach for protective group reactivity / T.I. Madzhidov, A.I. Lin, I. Antipin, O. Klimchuk, A. Varnek // Second Kazan Summer School in Chemoinformatics: July 6-9, 2015, Kazan, Russia: Book of Abstracts and Scientific Program. - Kazan, 2015. - P. 22.
• Madzhidov T.I. Structure-reactivity relationship in bimolecular elimination reactions based on the condensed graph of a reaction / T. I. Madzhidov, A. V. Bodrov, T. R. Gimadiev, R. I. Nugmanov, I. S. Antipin, A. A. Varnek // Journal of Structural Chemistry. - 2015. -V. 56. - Is. 7. - Pp. 1227-1234.
• Lin A.I., Madzhidov T.I., Nugmanov R.I., Antipin I.S., Klimchuk O., Varnek A.Prediction of Protective Groups reactivity and optimal conditions in catalytic hydrogenation reaction of deprotection, Second International School-Seminar From empirical to predictive chemistry: Kazan Federal University press, 2015, p.10.

• Нугманов, Р.И. Разработка моделей «структура-свойство» в реакциях нуклеофильного замещения с участием азидов / Р.И. Нугманов, Т.И. Маджидов, Г.Р. Халиуллина, И.И. Баскин, И.С. Антипин, А.А. Варнек - Журнал структурной химии. – 2014. – Т. 55, Вып. 6. – C. 1080–1087
• T. I. Madzhidov, P. G. Polishchuk, R. I. Nugmanov, A. V. Bodrov, A. I. Lin, I. I. Baskin, A. A. Varnek, I. S. Antipin. Structure–Reactivity Relationships in Terms of the Condensed Graphs of Reactions // Russian Journal of Organic Chemistry – 2014. - V.50, No. 4 - p. 459–463.
• Nugmanov R.I. Development of "structure-property" models in nucleophilic substitution reactions involving azides / Nugmanov, R.I., Madzhidov, T.I. , Khaliullina, G.R., Baskin, I.I., Antipin, I.S., Varnek, A.A. // Journal of Structural Chemistry. - 2014. - V. 55. - Is. 6. - Pp. 1026-1033.

• Polishchuk P.G. Estimation of the size of drug-like chemical space based on GDB-17 data / P.G. Polishchuk, T.I. Madzhidov, A. Varnek // Journal of Computer-Aided Molecular Design - 2013. - V. 27, Is. 8. - p. 675-679