Estimation of the size of drug-like chemical space based on GDB-17 data. - Pavel G. Polishchuk; Timur I. Madzhidov; Alexandre Varnek (J. Comput. Aided Mol. Des., 2013)

Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis. - Arkadii I. Lin; Timur I. Madzhidov; Olga Klimchuk; Ramil I. Nugmanov; Igor S. Antipin; Alexandre Varnek (J. Chem. Inf. Model., 2016)

Structure-reactivity modeling using mixture-based representation of chemical reactions. - Pavel G. Polishchuk; Timur I. Madzhidov; Timur Gimadiev; Andrey Bodrov; Ramil I. Nugmanov; Alexandre Varnek (J. Comput. Aided Mol. Des., 2017)

Assessment of tautomer distribution using the condensed reaction graph approach. - Timur Gimadiev; Timur I. Madzhidov; Ramil I. Nugmanov; Igor I. Baskin; Igor S. Antipin; Alexandre Varnek (J. Comput. Aided Mol. Des., 2018)

Hydration of copper(II) amino acids complexes. - Mikhail S. Bukharov; Valery G. Shtyrlin; Edward M. Gilyazetdinov; Nikita Yu. Serov; Timur I. Madzhidov (J. Comput. Chem., 2018)

Multi-instance Learning for Structure-Activity Modeling for Molecular Properties. - Dmitry V. Zankov; Maxim D. Shevelev; Alexandra V. Nikonenko; Pavel G. Polishchuk; Asima I. Rakhimbekova; Timur I. Madzhidov (AIST (Supplement), 2019)

CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing. - Ramil I. Nugmanov; Ravil N. Mukhametgaleev; Tagir Akhmetshin; Timur Gimadiev; Valentina A. Afonina; Timur I. Madzhidov; Alexandre Varnek (J. Chem. Inf. Model., 2019)

Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules. - Dmitry V. Zankov; Timur I. Madzhidov; Asima I. Rakhimbekova; Timur Gimadiev; Ramil I. Nugmanov; Marina A. Kazymova; Igor I. Baskin; Alexandre Varnek (J. Chem. Inf. Model., 2019)

Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data. - Timur Gimadiev; Ramil I. Nugmanov; Dinar Batyrshin; Timur I. Madzhidov; Satoshi Maeda; Pavel Sidorov; Alexandre Varnek (J. Chem. Inf. Model., 2021)

QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach. - Dmitry V. Zankov; Mariia Matveieva; Aleksandra V. Nikonenko; Ramil I. Nugmanov; Igor I. Baskin; Alexandre Varnek; Pavel G. Polishchuk; Timur I. Madzhidov (J. Chem. Inf. Model., 2021)

HyFactor: A Novel Open-Source, Graph-Based Architecture for Chemical Structure Generation. - Tagir Akhmetshin; Arkadii I. Lin; Daniyar Mazitov; Yuliana Zabolotna; Evgenii Ziaikin; Timur I. Madzhidov; Alexandre Varnek (J. Chem. Inf. Model., 2022)

Inverse QSAR: Reversing Descriptor-Driven Prediction Pipeline Using Attention-Based Conditional Variational Autoencoder. - William Bort; Daniyar Mazitov; Dragos Horvath; Fanny Bonachéra; Arkadii I. Lin; Gilles Marcou; Igor I. Baskin; Timur I. Madzhidov; Alexandre Varnek (J. Chem. Inf. Model., 2022)

CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data. - Timur Gimadiev; Ramil I. Nugmanov; Aigul Khakimova; Adeliya Fatykhova; Timur I. Madzhidov; Pavel Sidorov; Alexandre Varnek (J. Chem. Inf. Model., 2022)

Multi-Instance Learning Approach to the Modeling of Enantioselectivity of Conformationally Flexible Organic Catalysts. - Dmitry V. Zankov; Timur I. Madzhidov; Pavel G. Polishchuk; Pavel Sidorov; Alexandre Varnek (J. Chem. Inf. Model., 2023)

SynPlanner: An End-to-End Tool for Synthesis Planning. - Tagir Akhmetshin; Dmitry V. Zankov; Philippe Gantzer; Dmitry Babadeev; Anna Pinigina; Timur I. Madzhidov; Alexandre Varnek (J. Chem. Inf. Model., 2025)