An Application of the Miertus-Scrocco-Tomasi Solvation Model in Molecular Mechanics and Dynamics Simulations. - Alexandre Varnek; Georges Wipff; A. S. Glebov; D. Feil (J. Comput. Chem., 1995)

Theoretical calculations of extraction selectivity: Alkali cation complexes of calix[4]-bis-crown6 in pure water, chloroform, and at a water/chloroform interface. - Alexandre Varnek; Georges Wipff (J. Comput. Chem., 1996)

A fast and Space-Efficient boundary element method for computing electrostatic and hydration effects in large molecules. - Randy J. Zauhar; Alexandre Varnek (J. Comput. Chem., 1996)

van der Waals host-guest complexes: Can one predict complexation selectivity of neutral guests by a cryptophane? MD-FEP studies in gas phase and chloroform solution. - Alexandre Varnek; Severine Helissen; Georges Wipff; André Collet (J. Comput. Chem., 1998)

Modeling of Ion Complexation and Extraction Using Substructural Molecular Fragments. - Vitaly P. Solov'ev; Alexandre Varnek; Georges Wipff (J. Chem. Inf. Comput. Sci., 2000)

Assessment of the Macrocyclic Effect for the Complexation of Crown-Ethers with Alkali Cations Using the Substructural Molecular Fragments Method. - Alexandre Varnek; Georges Wipff; Vitaly P. Solov'ev; A. F. Solotnov (J. Chem. Inf. Comput. Sci., 2002)

Anti-HIV Activity of HEPT, TIBO, and Cyclic Urea Derivatives: Structure-Property Studies, Focused Combinatorial Library Generation, and Hits Selection Using Substructural Molecular Fragments Method. - Vitaly P. Solov'ev; Alexandre Varnek (J. Chem. Inf. Comput. Sci., 2003)

Quantitative Structure-Property Relationship Modeling of beta-Cyclodextrin Complexation Free Energies. - Alan R. Katritzky; Dan C. Fara; Hongfang Yang; Mati Karelson; Takahiro Suzuki; Vitaly P. Solov'ev; Alexandre Varnek (J. Chem. Inf. Model., 2004)

"In Silico" Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands: QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests. - Alexandre Varnek; Denis Fourches; Vitaly P. Solov'ev; Vladimir E. Baulin; Alexander N. Turanov; Vasili K. Karandashev; Dan C. Fara; Alan R. Katritzky (J. Chem. Inf. Model., 2004)

Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures. - Alexandre Varnek; Denis Fourches; Frank Hoonakker; Vitaly P. Solov'ev (J. Comput. Aided Mol. Des., 2005)

Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores. - Igor V. Tetko; Vitaly P. Solov'ev; Alexey V. Antonov; Xiaojun Yao; Jean-Pierre Doucet; Bo Tao Fan; Frank Hoonakker; Denis Fourches; Piere Jost; Nicolas Lachiche; Alexandre Varnek (J. Chem. Inf. Model., 2006)

Stochastic versus Stepwise Strategies for Quantitative Structure-Activity Relationship GenerationHow Much Effort May the Mining for Successful QSAR Models Take? - Dragos Horvath; Fanny Bonachéra; Vitaly P. Solov'ev; Cédric Gaudin; Alexandre Varnek (J. Chem. Inf. Model., 2007)

Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points? - Alexandre Varnek; Natalia V. Kireeva; Igor V. Tetko; Igor I. Baskin; Vitaly P. Solov'ev (J. Chem. Inf. Model., 2007)

Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection. - Igor V. Tetko; Iurii Sushko; Anil Kumar Pandey; Hao Zhu 012; Alexander Tropsha; Ester Papa; Tomas Öberg; Roberto Todeschini; Denis Fourches; Alexandre Varnek (J. Chem. Inf. Model., 2008)

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. - Hao Zhu 012; Alexander Tropsha; Denis Fourches; Alexandre Varnek; Ester Papa; Paola Gramatica; Tomas Öberg; Phuong Dao; Artem Cherkasov; Igor V. Tetko (J. Chem. Inf. Model., 2008)

Predicting the Predictability: A Unified Approach to the Applicability Domain Problem of QSAR Models. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2009)

Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients. - Alexandre Varnek; Cédric Gaudin; Gilles Marcou; Igor I. Baskin; Anil Kumar Pandey; Igor V. Tetko (J. Chem. Inf. Model., 2009)

A Representation to Apply Usual Data Mining Techniques to Chemical Reactions. - Frank Hoonakker; Nicolas Lachiche; Alexandre Varnek; Alain Wagner (IEA/AIE (2), 2010)

A unified approach to the applicability domain problem of QSAR models. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Cheminformatics, 2010)

Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset. - Gilles Marcou; Nicolas Lachiche; L. Brillet; J.-M. Paris; Alexandre Varnek (J. Cheminformatics, 2010)

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. - Iurii Sushko; Sergii Novotarskyi; Robert Körner; Anil Kumar Pandey; Artem Cherkasov; Jiazhong Li; Paola Gramatica; Katja Hansen; Timon Schroeter; Klaus-Robert Müller; Lili Xi; Huanxiang Liu; et al. (J. Chem. Inf. Model., 2010)

A Representation to Apply Usual Data Mining Techniques to Chemical reactions - Illustration on the Rate Constant of SN2 reactions in water. - Frank Hoonakker; Nicolas Lachiche; Alexandre Varnek; Alain Wagner (Int. J. Artif. Intell. Tools, 2011)

Local neighborhood behavior in a combinatorial library context. - Dragos Horvath; Christian J. Koch; Gisbert Schneider; Gilles Marcou; Alexandre Varnek (J. Comput. Aided Mol. Des., 2011)

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. - Iurii Sushko; Sergii Novotarskyi; Robert Körner; Anil Kumar Pandey; Matthias Rupp; Wolfram Teetz; Stefan Brandmaier; Ahmed Abdelaziz; Volodymyr V. Prokopenko; Vsevolod Yu. Tanchuk; Roberto Todeschini; Alexandre Varnek; et al. (J. Comput. Aided Mol. Des., 2011)

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. - Iurii Sushko; Anil Kumar Pandey; Sergii Novotarskyi; Robert Körner; Matthias Rupp; Wolfram Teetz; Stefan Brandmaier; Ahmed Abdelaziz; Volodymyr V. Prokopenko; Vsevolod Yu. Tanchuk; Roberto Todeschini; Alexandre Varnek; et al. (J. Cheminformatics, 2011)

Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches. - Aurélie de Luca; Dragos Horvath; Gilles Marcou; Vitaly P. Solov'ev; Alexandre Varnek (J. Chem. Inf. Model., 2012)

Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms. - Christophe Muller; Gilles Marcou; Dragos Horvath; João Aires-de-Sousa; Alexandre Varnek (J. Chem. Inf. Model., 2012)

Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis? - Alexandre Varnek; Igor I. Baskin (J. Chem. Inf. Model., 2012)

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)

Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints. - Vladimir I. Chupakhin; Gilles Marcou; Igor I. Baskin; Alexandre Varnek; Didier Rognan (J. Chem. Inf. Model., 2013)

Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS). - Héléna A. Gaspar; Gilles Marcou; Dragos Horvath; Alban Arrault; Sylvain Lozano; Philippe Vayer; Alexandre Varnek (J. Chem. Inf. Model., 2013)

Do Not Hesitate to Use Tversky - and Other Hints for Successful Active Analogue Searches with Feature Count Descriptors. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2013)

Computational chemogenomics: Is it more than inductive transfer? - J. B. Brown; Yasushi Okuno; Gilles Marcou; Alexandre Varnek; Dragos Horvath (J. Comput. Aided Mol. Des., 2014)

QSPR ensemble modelling of the 1: 1 and 1: 2 complexation of Co2+, Ni2+, and Cu2+ with organic ligands: relationships between stability constants. - Vitaly P. Solov'ev; Alexandre Varnek; Aslan Yu. Tsivadze (J. Comput. Aided Mol. Des., 2014)

Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds. - Pavel Sidorov; Héléna A. Gaspar; Gilles Marcou; Alexandre Varnek; Dragos Horvath (J. Comput. Aided Mol. Des., 2015)

Continuous indicator fields: a novel universal type of molecular fields. - Gleb V. Sitnikov; Nelly I. Zhokhova; Yury A. Ustynyuk; Alexandre Varnek; Igor I. Baskin (J. Comput. Aided Mol. Des., 2015)

Chemical Data Visualization and Analysis with Incremental Generative Topographic Mapping: Big Data Challenge. - Héléna A. Gaspar; Igor I. Baskin; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2015)

Stargate GTM: Bridging Descriptor and Activity Spaces. - Héléna A. Gaspar; Igor I. Baskin; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2015)

Expert System for Predicting Reaction Conditions: The Michael Reaction Case. - Gilles Marcou; João Aires-de-Sousa; Diogo A. R. S. Latino; Aurélie de Luca; Dragos Horvath; V. Rietsch; Alexandre Varnek (J. Chem. Inf. Model., 2015)

Prediction of Activity Cliffs Using Condensed Graphs of Reaction Representations, Descriptor Recombination, Support Vector Machine Classification, and Support Vector Regression. - Dragos Horvath; Gilles Marcou; Alexandre Varnek; Shilva Kayastha; Antonio de la Vega de León; Jürgen Bajorath (J. Chem. Inf. Model., 2016)

Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set. - Kyrylo Klimenko; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2016)

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)

Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks. - Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2016)

Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis. - Pavel G. Polishchuk; Oleg Tinkov; Tatiana Khristova; Liudmila Ognichenko; Anna Kosinskaya; Alexandre Varnek; Victor Kuzmin (J. Chem. Inf. Model., 2016)

Predictive cartography of metal binders using generative topographic mapping. - Igor I. Baskin; Vitaly P. Solov'ev; Alexander A. Bagatur'yants; Alexandre Varnek (J. Comput. Aided Mol. Des., 2017)

From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets. - Shilva Kayastha; Ryo Kunimoto; Dragos Horvath; Alexandre Varnek; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2017)

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)

QSAR modeling and chemical space analysis of antimalarial compounds. - Pavel Sidorov; Birgit Viira; Elisabeth Davioud-Charvet; Uko Maran; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Comput. Aided Mol. Des., 2017)

Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps. - Shilva Kayastha; Dragos Horvath; Erik Gilberg; Michael Gütschow; Jürgen Bajorath; Alexandre Varnek (J. Chem. Inf. Model., 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)

Rescoring of docking poses under Occam's Razor: are there simpler solutions? - Michael Zhenin; Malkeet Singh Bahia; Gilles Marcou; Alexandre Varnek; Hanoch Senderowitz; Dragos Horvath (J. Comput. Aided Mol. Des., 2018)

Multi-task generative topographic mapping in virtual screening. - Arkadii I. Lin; Dragos Horvath; Gilles Marcou; Bernd Beck; Alexandre Varnek (J. Comput. Aided Mol. Des., 2019)

Virtual Screening with Generative Topographic Maps: How Many Maps Are Required? - Iuri Casciuc; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Jürgen Bajorath; Alexandre Varnek (J. Chem. Inf. Model., 2019)

CovaDOTS: In Silico Chemistry-Driven Tool to Design Covalent Inhibitors Using a Linking Strategy. - Laurent Hoffer; Magali Saez-Ayala; Dragos Horvath; Alexandre Varnek; Xavier Morelli; Philippe Roche (J. Chem. Inf. Model., 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)

De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping. - Boris Sattarov; Igor I. Baskin; Dragos Horvath; Gilles Marcou; Esben Jannik Bjerrum; 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)

Diversifying chemical libraries with generative topographic mapping. - Arkadii I. Lin; Bernd Beck; Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Comput. Aided Mol. Des., 2020)

"Big Data" Fast Chemoinformatics Model to Predict Generalized Born Radius and Solvent Accessibility as a Function of Geometry. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2020)

Trustworthiness, the Key to Grid-Based Map-Driven Predictive Model Enhancement and Applicability Domain Control. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2020)

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)

Chemography: Searching for Hidden Treasures. - Yuliana Zabolotna; Arkadii I. Lin; Dragos Horvath; Gilles Marcou; Dmitriy M. Volochnyuk; 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)

HIV-1 drug resistance profiling using amino acid sequence space cartography. - Karina Pikalyova; Alexey Orlov; Arkadii I. Lin; Olga A. Tarasova; Gilles Marcou; Dragos Horvath; Vladimir Poroikov; Alexandre Varnek (Bioinform., 2022)

Implementation of a soft grading system for chemistry in a Moodle plugin. - Louis Plyer; Gilles Marcou; Céline Perves; Rachel Schurhammer; Alexandre Varnek (J. Cheminformatics, 2022)

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)

Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery. - Yuliana Zabolotna; Fanny Bonachéra; Dragos Horvath; Arkadii I. Lin; Gilles Marcou; Olga Klimchuk; Alexandre Varnek (J. Chem. Inf. Model., 2022)

SynthI: A New Open-Source Tool for Synthon-Based Library Design. - Yuliana Zabolotna; Dmitriy M. Volochnyuk; Sergey V. Ryabukhin; Kostiantyn Gavrylenko; Dragos Horvath; Olga Klimchuk; Oleksandr Oksiuta; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2022)

A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry. - Yuliana Zabolotna; Dmitriy M. Volochnyuk; Sergey V. Ryabukhin; Dragos Horvath; Konstantin S. Gavrilenko; Gilles Marcou; Yurii S. Moroz; Oleksandr Oksiuta; Alexandre Varnek (J. Chem. Inf. Model., 2022)

Chemical Library Space: Definition and DNA-Encoded Library Comparison Study Case. - Regina Pikalyova; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2023)

GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design. - Giuseppe Lamanna; Pietro Delre; Gilles Marcou; Michele Saviano; Alexandre Varnek; Dragos Horvath; Giuseppe Felice Mangiatordi (J. Chem. Inf. Model., 2023)

Meta-GTM: Visualization and Analysis of the Chemical Library Space. - Regina Pikalyova; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2023)

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)

School of cheminformatics in Latin America. - Karla Gonzalez-Ponce; Carolina Horta Andrade; Fiona M. I. Hunter; Johannes Kirchmair; Karina Martínez-Mayorga; José L. Medina-Franco; Matthias Rarey; Alexander Tropsha; Alexandre Varnek; Barbara Zdrazil (J. Cheminformatics, 2023)

Combinatorial Library Neural Network (CoLiNN) for Combinatorial Library Visualization Without Compound Enumeration. - Regina Pikalyova; Tagir Akhmetshin; Dragos Horvath; Alexandre Varnek (ICANN (10), 2024)

De Novo Drug Design - Do We Really Want to Be "Original"? - A Real-world Case Study on Colchicine-Site Tubulin Binders. - Maxim Shevelev; Dragos Horvath; Gilles Marcou; Alexandre Varnek (ICANN (10), 2024)

Implementation of a soft grading system for chemistry in a Moodle plugin: reaction handling. - Louis Plyer; Gilles Marcou; Céline Perves; Fanny Bonachéra; Alexandre Varnek (J. Cheminformatics, 2024)

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)

Higher education in chemoinformatics: achievements and challenges. - Alexandre Varnek; Gilles Marcou; Dragos Horvath (J. Cheminformatics, 2025)