Alexandre Varnek

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 37

Top Topics

Support Vector Machine Classification

Generative Topographic Mapping

Virtual Screening

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Cheminformatics

Publications

Giuseppe Lamanna, Pietro Delre, Gilles Marcou, Michele Saviano, Alexandre Varnek, Dragos Horvath, Giuseppe Felice Mangiatordi
GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design. J. Chem. Inf. Model. 63 (16) (2023)
Regina Pikalyova, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Alexandre Varnek
Meta-GTM: Visualization and Analysis of the Chemical Library Space. J. Chem. Inf. Model. 63 (17) (2023)
Dmitry V. Zankov, Timur I. Madzhidov, Pavel G. Polishchuk, Pavel Sidorov, Alexandre Varnek
Multi-Instance Learning Approach to the Modeling of Enantioselectivity of Conformationally Flexible Organic Catalysts. J. Chem. Inf. Model. 63 (21) (2023)
Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona Hunter, Johannes Kirchmair, Karina Martínez-Mayorga, José L. Medina-Franco, Matthias Rarey, Alexander Tropsha, Alexandre Varnek, Barbara Zdrazil
School of cheminformatics in Latin America. J. Cheminformatics 15 (1) (2023)
Regina Pikalyova, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Alexandre Varnek
Chemical Library Space: Definition and DNA-Encoded Library Comparison Study Case. J. Chem. Inf. Model. 63 (13) (2023)
Yuliana Zabolotna, Dmitriy M. Volochnyuk, Sergey V. Ryabukhin, Dragos Horvath, Konstantin S. Gavrilenko, Gilles Marcou, Yurii S. Moroz, Oleksandr Oksiuta, Alexandre Varnek
A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry. J. Chem. Inf. Model. 62 (9) (2022)
Tagir Akhmetshin, Arkadii I. Lin, Daniyar Mazitov, Yuliana Zabolotna, Evgenii Ziaikin, Timur I. Madzhidov, Alexandre Varnek
HyFactor: A Novel Open-Source, Graph-Based Architecture for Chemical Structure Generation. J. Chem. Inf. Model. 62 (15) (2022)
Yuliana Zabolotna, Dmitriy M. Volochnyuk, Sergey V. Ryabukhin, Kostiantyn Gavrylenko, Dragos Horvath, Olga Klimchuk, Oleksandr Oksiuta, Gilles Marcou, Alexandre Varnek
SynthI: A New Open-Source Tool for Synthon-Based Library Design. J. Chem. Inf. Model. 62 (9) (2022)
Yuliana Zabolotna, Fanny Bonachéra, Dragos Horvath, Arkadii I. Lin, Gilles Marcou, Olga Klimchuk, Alexandre Varnek
Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery. J. Chem. Inf. Model. 62 (18) (2022)
Louis Plyer, Gilles Marcou, Céline Perves, Rachel Schurhammer, Alexandre Varnek
Implementation of a soft grading system for chemistry in a Moodle plugin. J. Cheminformatics 14 (1) (2022)
Karina Pikalyova, Alexey Orlov, Arkadii I. Lin, Olga A. Tarasova, Gilles Marcou, Dragos Horvath, Vladimir Poroikov, Alexandre Varnek
HIV-1 drug resistance profiling using amino acid sequence space cartography. Bioinform. 38 (8) (2022)
William Bort, Daniyar Mazitov, Dragos Horvath, Fanny Bonachéra, Arkadii I. Lin, Gilles Marcou, Igor I. Baskin, Timur I. Madzhidov, Alexandre Varnek
Inverse QSAR: Reversing Descriptor-Driven Prediction Pipeline Using Attention-Based Conditional Variational Autoencoder. J. Chem. Inf. Model. 62 (22) (2022)
Timur Gimadiev, Ramil I. Nugmanov, Aigul Khakimova, Adeliya Fatykhova, Timur I. Madzhidov, Pavel Sidorov, Alexandre Varnek
CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data. J. Chem. Inf. Model. 62 (9) (2022)
Timur Gimadiev, Ramil I. Nugmanov, Dinar Batyrshin, Timur I. Madzhidov, Satoshi Maeda, Pavel Sidorov, Alexandre Varnek
Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data. J. Chem. Inf. Model. 61 (2) (2021)
Dmitry V. Zankov, Mariia Matveieva, Aleksandra V. Nikonenko, Ramil I. Nugmanov, Igor I. Baskin, Alexandre Varnek, Pavel G. Polishchuk, Timur I. Madzhidov
QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach. J. Chem. Inf. Model. 61 (10) (2021)
Yuliana Zabolotna, Arkadii I. Lin, Dragos Horvath, Gilles Marcou, Dmitriy M. Volochnyuk, Alexandre Varnek
Chemography: Searching for Hidden Treasures. J. Chem. Inf. Model. 61 (1) (2021)
Dragos Horvath, Gilles Marcou, Alexandre Varnek
Trustworthiness, the Key to Grid-Based Map-Driven Predictive Model Enhancement and Applicability Domain Control. J. Chem. Inf. Model. 60 (12) (2020)
Dragos Horvath, Gilles Marcou, Alexandre Varnek
"Big Data" Fast Chemoinformatics Model to Predict Generalized Born Radius and Solvent Accessibility as a Function of Geometry. J. Chem. Inf. Model. 60 (6) (2020)
Arkadii I. Lin, Bernd Beck, Dragos Horvath, Gilles Marcou, Alexandre Varnek
Diversifying chemical libraries with generative topographic mapping. J. Comput. Aided Mol. Des. 34 (7) (2020)
Dmitry V. Zankov, Timur I. Madzhidov, Asima I. Rakhimbekova, Timur Gimadiev, Ramil I. Nugmanov, Marina A. Kazymova, Igor I. Baskin, Alexandre Varnek
Conjugated Quantitative Structure-Property Relationship Models: Application to Simultaneous Prediction of Tautomeric Equilibrium Constants and Acidity of Molecules. J. Chem. Inf. Model. 59 (11) (2019)
Boris Sattarov, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Esben Jannik Bjerrum, Alexandre Varnek
De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping. J. Chem. Inf. Model. 59 (3) (2019)
Iuri Casciuc, Yuliana Zabolotna, Dragos Horvath, Gilles Marcou, Jürgen Bajorath, Alexandre Varnek
Virtual Screening with Generative Topographic Maps: How Many Maps Are Required? J. Chem. Inf. Model. 59 (1) (2019)
Ramil I. Nugmanov, Ravil N. Mukhametgaleev, Tagir Akhmetshin, Timur Gimadiev, Valentina A. Afonina, Timur I. Madzhidov, Alexandre Varnek
CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing. J. Chem. Inf. Model. 59 (6) (2019)
Laurent Hoffer, Magali Saez-Ayala, Dragos Horvath, Alexandre Varnek, Xavier Morelli, Philippe Roche
CovaDOTS: In Silico Chemistry-Driven Tool to Design Covalent Inhibitors Using a Linking Strategy. J. Chem. Inf. Model. 59 (4) (2019)
Arkadii I. Lin, Dragos Horvath, Gilles Marcou, Bernd Beck, Alexandre Varnek
Multi-task generative topographic mapping in virtual screening. J. Comput. Aided Mol. Des. 33 (3) (2019)
Michael Zhenin, Malkeet Singh Bahia, Gilles Marcou, Alexandre Varnek, Hanoch Senderowitz, Dragos Horvath
Rescoring of docking poses under Occam's Razor: are there simpler solutions? J. Comput. Aided Mol. Des. 32 (9) (2018)
Timur Gimadiev, Timur I. Madzhidov, Ramil I. Nugmanov, Igor I. Baskin, Igor S. Antipin, Alexandre Varnek
Assessment of tautomer distribution using the condensed reaction graph approach. J. Comput. Aided Mol. Des. 32 (3) (2018)
Pavel G. Polishchuk, Timur I. Madzhidov, Timur Gimadiev, Andrey Bodrov, Ramil I. Nugmanov, Alexandre Varnek
Structure-reactivity modeling using mixture-based representation of chemical reactions. J. Comput. Aided Mol. Des. 31 (9) (2017)
Pavel Sidorov, Birgit Viira, Elisabeth Davioud-Charvet, Uko Maran, Gilles Marcou, Dragos Horvath, Alexandre Varnek
QSAR modeling and chemical space analysis of antimalarial compounds. J. Comput. Aided Mol. Des. 31 (5) (2017)
Shilva Kayastha, Ryo Kunimoto, Dragos Horvath, Alexandre Varnek, Jürgen Bajorath
From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets. J. Comput. Aided Mol. Des. 31 (11) (2017)
Shilva Kayastha, Dragos Horvath, Erik Gilberg, Michael Gütschow, Jürgen Bajorath, Alexandre Varnek
Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps. J. Chem. Inf. Model. 57 (5) (2017)
Igor I. Baskin, Vitaly P. Solov'ev, Alexander A. Bagatur'yants, Alexandre Varnek
Predictive cartography of metal binders using generative topographic mapping. J. Comput. Aided Mol. Des. 31 (8) (2017)
Arkadii I. Lin, Timur I. Madzhidov, Olga Klimchuk, Ramil I. Nugmanov, Igor S. Antipin, Alexandre Varnek
Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis. J. Chem. Inf. Model. 56 (11) (2016)
Pavel G. Polishchuk, Oleg Tinkov, Tatiana Khristova, Liudmila Ognichenko, Anna Kosinskaya, Alexandre Varnek, Victor Kuzmin
Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis. J. Chem. Inf. Model. 56 (8) (2016)
Gilles Marcou, Dragos Horvath, Alexandre Varnek
Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks. J. Chem. Inf. Model. 56 (1) (2016)
Kyrylo Klimenko, Gilles Marcou, Dragos Horvath, Alexandre Varnek
Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set. J. Chem. Inf. Model. 56 (8) (2016)
Dragos Horvath, Gilles Marcou, Alexandre Varnek, Shilva Kayastha, Antonio de la Vega de León, Jürgen Bajorath
Prediction of Activity Cliffs Using Condensed Graphs of Reaction Representations, Descriptor Recombination, Support Vector Machine Classification, and Support Vector Regression. J. Chem. Inf. Model. 56 (9) (2016)
Héléna A. Gaspar, Igor I. Baskin, Gilles Marcou, Dragos Horvath, Alexandre Varnek
Stargate GTM: Bridging Descriptor and Activity Spaces. J. Chem. Inf. Model. 55 (11) (2015)
Gleb V. Sitnikov, Nelly I. Zhokhova, Yury A. Ustynyuk, Alexandre Varnek, Igor I. Baskin
Continuous indicator fields: a novel universal type of molecular fields. J. Comput. Aided Mol. Des. 29 (3) (2015)
Pavel Sidorov, Héléna A. Gaspar, Gilles Marcou, Alexandre Varnek, Dragos Horvath
Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds. J. Comput. Aided Mol. Des. 29 (12) (2015)
Héléna A. Gaspar, Igor I. Baskin, Gilles Marcou, Dragos Horvath, Alexandre Varnek
Chemical Data Visualization and Analysis with Incremental Generative Topographic Mapping: Big Data Challenge. J. Chem. Inf. Model. 55 (1) (2015)
Gilles Marcou, João Aires-de-Sousa, Diogo A. R. S. Latino, Aurélie de Luca, Dragos Horvath, V. Rietsch, Alexandre Varnek
Expert System for Predicting Reaction Conditions: The Michael Reaction Case. J. Chem. Inf. Model. 55 (2) (2015)
J. B. Brown, Yasushi Okuno, Gilles Marcou, Alexandre Varnek, Dragos Horvath
Computational chemogenomics: Is it more than inductive transfer? J. Comput. Aided Mol. Des. 28 (6) (2014)
Vitaly P. Solov'ev, Alexandre Varnek, Aslan Yu. Tsivadze
QSPR ensemble modelling of the 1: 1 and 1: 2 complexation of Co2+, Ni2+, and Cu2+ with organic ligands: relationships between stability constants. J. Comput. Aided Mol. Des. 28 (5) (2014)
Dragos Horvath, Gilles Marcou, Alexandre Varnek
Do Not Hesitate to Use Tversky - and Other Hints for Successful Active Analogue Searches with Feature Count Descriptors. J. Chem. Inf. Model. 53 (7) (2013)
Héléna A. Gaspar, Gilles Marcou, Dragos Horvath, Alban Arrault, Sylvain Lozano, Philippe Vayer, Alexandre Varnek
Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS). J. Chem. Inf. Model. 53 (12) (2013)
Pavel G. Polishchuk, Timur I. Madzhidov, Alexandre Varnek
Estimation of the size of drug-like chemical space based on GDB-17 data. J. Comput. Aided Mol. Des. 27 (8) (2013)
Vladimir I. Chupakhin, Gilles Marcou, Igor I. Baskin, Alexandre Varnek, Didier Rognan
Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints. J. Chem. Inf. Model. 53 (4) (2013)
Aurélie de Luca, Dragos Horvath, Gilles Marcou, Vitaly P. Solov'ev, Alexandre Varnek
Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches. J. Chem. Inf. Model. 52 (9) (2012)
Christophe Muller, Gilles Marcou, Dragos Horvath, João Aires-de-Sousa, Alexandre Varnek
Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms. J. Chem. Inf. Model. 52 (12) (2012)
Alexandre Varnek, Igor I. Baskin
? J. Chem. Inf. Model. 52 (6) (2012)
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, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria Grishina, Johann Gasteiger, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Cheminformatics 3 (S-1) (2011)
Frank Hoonakker, Nicolas Lachiche, Alexandre Varnek, Alain Wagner
2 reactions in water. Int. J. Artif. Intell. Tools 20 (2) (2011)
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, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria Grishina, Johann Gasteiger, Christof H. Schwab, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav V. Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, João Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony J. Williams, Valery Tkachenko, Igor V. Tetko
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J. Comput. Aided Mol. Des. 25 (6) (2011)
Dragos Horvath, Christian J. Koch, Gisbert Schneider, Gilles Marcou, Alexandre Varnek
Local neighborhood behavior in a combinatorial library context. J. Comput. Aided Mol. Des. 25 (3) (2011)
Dragos Horvath, Gilles Marcou, Alexandre Varnek
A unified approach to the applicability domain problem of QSAR models. J. Cheminformatics 2 (S-1) (2010)
Frank Hoonakker, Nicolas Lachiche, Alexandre Varnek, Alain Wagner
A Representation to Apply Usual Data Mining Techniques to Chemical Reactions. IEA/AIE (2) (2010)
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, Xiaojun Yao, Tomas Öberg, Farhad Hormozdiari, Phuong Dao, Süleyman Cenk Sahinalp, Roberto Todeschini, Pavel G. Polishchuk, Anatoly G. Artemenko, Victor Kuzmin, Todd Martin, Douglas M. Young, Denis Fourches, Eugene N. Muratov, Alexander Tropsha, Igor I. Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexandre Varnek, Volodymyr V. Prokopenko, Igor V. Tetko
Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. J. Chem. Inf. Model. 50 (12) (2010)
Gilles Marcou, Nicolas Lachiche, L. Brillet, J.-M. Paris, Alexandre Varnek
Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset. J. Cheminformatics 2 (S-1) (2010)
Dragos Horvath, Gilles Marcou, Alexandre Varnek
Predicting the Predictability: A Unified Approach to the Applicability Domain Problem of QSAR Models. J. Chem. Inf. Model. 49 (7) (2009)
Alexandre Varnek, Cédric Gaudin, Gilles Marcou, Igor I. Baskin, Anil Kumar Pandey, Igor V. Tetko
Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients. J. Chem. Inf. Model. 49 (1) (2009)
Igor V. Tetko, Iurii Sushko, Anil Kumar Pandey, Hao Zhu, Alexander Tropsha, Ester Papa, Tomas Öberg, Roberto Todeschini, Denis Fourches, Alexandre Varnek
Focusing on Applicability Domain and Overfitting by Variable Selection. J. Chem. Inf. Model. 48 (9) (2008)
Hao Zhu, Alexander Tropsha, Denis Fourches, Alexandre Varnek, Ester Papa, Paola Gramatica, Tomas Öberg, Phuong Dao, Artem Cherkasov, Igor V. Tetko
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis. J. Chem. Inf. Model. 48 (4) (2008)
Alexandre Varnek, Natalia Kireeva, Igor V. Tetko, Igor I. Baskin, Vitaly P. Solov'ev
Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points? J. Chem. Inf. Model. 47 (3) (2007)
Dragos Horvath, Fanny Bonachéra, Vitaly P. Solov'ev, Cédric Gaudin, Alexandre Varnek
Stochastic versus Stepwise Strategies for Quantitative Structure-Activity Relationship GenerationHow Much Effort May the Mining for Successful QSAR Models Take? J. Chem. Inf. Model. 47 (3) (2007)
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
Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores. J. Chem. Inf. Model. 46 (2) (2006)
Alexandre Varnek, Denis Fourches, Frank Hoonakker, Vitaly P. Solov'ev
Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures. J. Comput. Aided Mol. Des. 19 (9-10) (2005)
Alexandre Varnek, Denis Fourches, Vitaly P. Solov'ev, Vladimir E. Baulin, Alexander N. Turanov, Vasili K. Karandashev, Dan C. Fara, Alan R. Katritzky
"In Silico" Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands: QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests. J. Chem. Inf. Model. 44 (4) (2004)
Alan R. Katritzky, Dan C. Fara, Hongfang Yang, Mati Karelson, Takahiro Suzuki, Vitaly P. Solov'ev, Alexandre Varnek
-Cyclodextrin Complexation Free Energies. J. Chem. Inf. Model. 44 (2) (2004)
Vitaly P. Solov'ev, Alexandre Varnek
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. J. Chem. Inf. Comput. Sci. 43 (5) (2003)
Alexandre Varnek, Georges Wipff, Vitaly P. Solov'ev, A. F. Solotnov
Assessment of the Macrocyclic Effect for the Complexation of Crown-Ethers with Alkali Cations Using the Substructural Molecular Fragments Method. J. Chem. Inf. Comput. Sci. 42 (4) (2002)
Vitaly P. Solov'ev, Alexandre Varnek, Georges Wipff
Modeling of Ion Complexation and Extraction Using Substructural Molecular Fragments. J. Chem. Inf. Comput. Sci. 40 (3) (2000)
Alexandre Varnek, Severine Helissen, Georges Wipff, André Collet
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. J. Comput. Chem. 19 (8) (1998)
Alexandre Varnek, Georges Wipff
Theoretical calculations of extraction selectivity: Alkali cation complexes of calix[4]-bis-crown6 in pure water, chloroform, and at a water/chloroform interface. J. Comput. Chem. 17 (13) (1996)
Randy J. Zauhar, Alexandre Varnek
A fast and Space-Efficient boundary element method for computing electrostatic and hydration effects in large molecules. J. Comput. Chem. 17 (7) (1996)
Alexandre Varnek, Georges Wipff, A. S. Glebov, D. Feil
An Application of the Miertus-Scrocco-Tomasi Solvation Model in Molecular Mechanics and Dynamics Simulations. J. Comput. Chem. 16 (1) (1995)