A. Varnek

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Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps

Jürgen Bajorath, Alexandre Varnek, Dragos Horvath, 2017, J. Chem. Inf. Model..

ISIDA - Platform for Virtual Screening Based on Fragment and Pharmacophoric Descriptors

I. Tetko, D. Fourches, D. Horvath, 2008 .

ISIDA Property‐Labelled Fragment Descriptors

D. Horvath, A. Varnek, G. Marcou, 2010, Molecular informatics.

Successful “In Silico” Design of New Efficient Uranyl Binders

D. Fourches, A. Varnek, O. Klimchuk, 2007 .

Data Curation

A. Varnek, G. Marcou, 2019, Encyclopedia of Big Data Technologies.

Publicly available QSPR models for environmental media persistence

E. Van Miert, A. Varnek, G. Marcou, 2020, SAR and QSAR in environmental research.

Mapping of the Available Chemical Space versus the Chemical Universe of Lead‐Like Compounds

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2018, ChemMedChem.

In silico Design, Virtual Screening and Synthesis of Novel Electrolytic Solvents

D. Horvath, A. Varnek, G. Marcou, 2019, Molecular informatics.

Quantitative Structure–Property Relationship (QSPR) Modeling of Normal Boiling Point Temperature and Composition of Binary Azeotropes

A. Varnek, V. Solov'ev, G. Marcou, 2011 .

A fast and Space‐efficient boundary element method for computing electrostatic and hydration effects in large molecules

A. Varnek, Randy J. Zauhar, R. Zauhar, 1996 .

QSAR modeling: where have you been? Where are you going to?

J. Dearden, R. Todeschini, R. Cramer, 2014, Journal of medicinal chemistry.

Autoignition temperature: comprehensive data analysis and predictive models

D. Horvath, A. Varnek, G. Marcou, 2020, SAR and QSAR in environmental research.

Integrated Strategy for Lead Optimization Based on Fragment Growing: The Diversity-Oriented-Target-Focused-Synthesis Approach.

D. Horvath, A. Varnek, P. Roche, 2018, Journal of medicinal chemistry.

Prediction of Aromatic Hydroxylation Sites for Human CYP1A2 Substrates Using Condensed Graph of Reactions

A. Varnek, G. Marcou, Christophe Muller, 2018 .

Development of “structure-property” models in nucleophilic substitution reactions involving azides

Igor I. Baskin, A. Varnek, Timur I. Madzhidov, 2014, Journal of Structural Chemistry.

Structure-reactivity relationships in terms of the condensed graphs of reactions

Igor I. Baskin, Alexandre Varnek, Timur I. Madzhidov, 2014, Russian Journal of Organic Chemistry.

Structure–reactivity relationship in bimolecular elimination reactions based on the condensed graph of a reaction

Timur I. Madzhidov, R. I. Nugmanov, Igor S. Antipin, 2015, Journal of Structural Chemistry.

Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms

Dragos Horvath, Gilles Marcou, Christophe Muller, 2012, J. Chem. Inf. Model..

Bimolecular Nucleophilic Substitution Reactions: Predictive Models for Rate Constants and Molecular Reaction Pairs Analysis

Alexandre Varnek, Timur Gimadiev, Pavel Polishchuk, 2018, Molecular informatics.

Structure–reactivity relationship in Diels–Alder reactions obtained using the condensed reaction graph approach

Igor I. Baskin, A. Varnek, Timur I. Madzhidov, 2017, Journal of Structural Chemistry.

QSPR Approach to Predict Nonadditive Properties of Mixtures. Application to Bubble Point Temperatures of Binary Mixtures of Liquids

G Marcou, A Varnek, E. Muratov, 2012, Molecular informatics.

Simple Ligand–Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison

Gilles Marcou, Alexandre Varnek, Héléna A. Gaspar, 2014, Computational and structural biotechnology journal.

In silico design of new ionic liquids based on quantitative structure-property relationship models of ionic liquid viscosity.

G Marcou, A Varnek, A. Varnek, 2011, The journal of physical chemistry. B.

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

Ruili Huang, Igor V. Tetko, Eva Bay Wedebye, 2016, Environmental health perspectives.

Structure-property modelling of complex formation of strontium with organic ligands in water

A. Yu. Tsivadze, A. Varnek, V. Solov'ev, 2006 .

Getting to Know the Neighbours with GTM: The Case of Antiviral Compounds

V. A. Palyulin, D. Horvath, A. Varnek, 2019, Molecular informatics.

Predictive Models for Kinetic Parameters of Cycloaddition Reactions

D. Horvath, A. Varnek, G. Marcou, 2018, Molecular informatics.

Generative topographic mapping in drug design.

D. Horvath, A. Varnek, G. Marcou, 2019, Drug discovery today. Technologies.

Publicly available models to predict normal boiling point of organic compounds

D. Horvath, A. Varnek, G. Marcou, 2013 .

Complexation of Mn2+, Fe2+, Y3+, La3+, Pb2+, and UO22+ with Organic Ligands: QSPR Ensemble Modeling of Stability Constants

A. Varnek, V. Solov'ev, G. Marcou, 2012 .

Stability constants of complexes of Zn2+, Cd2+, and Hg2+ with organic ligands: QSPR consensus modeling and design of new metal binders

A. Varnek, V. Solov'ev, G. Marcou, 2012, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

QSPR modeling of potentiometric sensitivity towards heavy metal ions for polymeric membrane sensors

A. Legin, A. Varnek, D. Kirsanov, 2019 .

Redox Polypharmacology as an Emerging Strategy to Combat Malarial Parasites

E. Davioud‐Charvet, D. Horvath, A. Varnek, 2016, ChemMedChem.

Design, Virtual Screening, and Synthesis of Antagonists of αIIbβ3 as Antiplatelet Agents.

V. M. Kabanov, Tetiana M. Khristova, T. Langer, 2015, Journal of medicinal chemistry.

Consensus QSAR models estimating acute toxicity to aquatic organisms from different trophic levels: algae, Daphnia and fish

E. Van Miert, A. Varnek, G. Marcou, 2020, SAR and QSAR in environmental research.

Predictive Models for the Free Energy of Hydrogen Bonded Complexes with Single and Cooperative Hydrogen Bonds

D. Horvath, A. Varnek, V. Solov'ev, 2016, Molecular informatics.

Thermodynamic radii of lanthanide ions derived from metal–ligand complexes stability constants

A. Varnek, V. Solov'ev, 2020, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

QSPR Modeling of Potentiometric Mg 2+ /Ca 2+ Selectivity for PVC‐plasticized Sensor Membranes

A. Legin, A. Varnek, V. Solov'ev, 2020 .

ehp CERAPP : Collaborative Estrogen Receptor Activity Prediction Project

Ruili Huang, Igor V. Tetko, Eva Bay Wedebye, 2016 .

Visualization and Analysis of Complex Reaction Data: The Case of Tautomeric Equilibria

D. Horvath, A. Varnek, G. Marcou, 2018, Molecular informatics.

QSPR Models on Fragment Descriptors

A. Varnek, V. Solov'ev, 2017 .

Classification of Metal Binders by Naïve Bayes Classifier on the Base of Molecular Fragment Descriptors and Ensemble Modeling

A. Varnek, V. Solov'ev, G. Marcou, 2019, Molecular informatics.

A. Varnek, G. Marcou, S. Pieraccini, 2022, International journal of molecular sciences.

Atom‐to‐atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies

Arkadii I. Lin, H. Ceulemans, A. Varnek, 2020, Molecular informatics.

A Summer School for Structuring the Chemoinformatics Community

Didier Rognan, Alexandre Varnek, D. Rognan, 2014, Molecular informatics.

Quantitative structure-property relationship modeling: a valuable support in high-throughput screening quality control.

Fiorella Ruggiu, Patrick Gizzi, Jacques Haiech, 2014, Analytical chemistry.

QSAR Modeling Based on Conformation Ensembles Using a Multi-Instance Learning Approach

A. Varnek, I. Baskin, P. Polishchuk, 2020, J. Chem. Inf. Model..

Fragment Descriptors in Virtual Screening

A. Varnek, I. Baskin, 2013, 1311.3723.

In Vitro Evaluation of In Silico Screening Approaches in Search for Selective ACE2 Binding Chemical Probes

D. Horvath, A. Varnek, O. Klimchuk, 2022, Molecules.

A Chemographic Audit of anti‐Coronavirus Structure‐activity Information from Public Databases (ChEMBL)

D. Horvath, A. Varnek, G. Marcou, 2020, Molecular informatics.

Electronic, spectroscopic, and ion-sensing properties of a dehydro[m]pyrido[14]- and [15]annulene isomer library.

A. Varnek, J. Gisselbrecht, A. Al Ouahabi, 2012, The Journal of organic chemistry.

In Silico Mining for Antimalarial Structure-Activity Knowledge and Discovery of Novel Antimalarial Curcuminoids

E. Davioud‐Charvet, D. Horvath, A. Varnek, 2016, Molecules.

Consensus models to predict oral rat acute toxicity and validation on a dataset coming from the industrial context

D. Horvath, E. Van Miert, A. Varnek, 2019, SAR and QSAR in environmental research.

RGD mimetics containing phthalimidine fragment as novel ligands of fibrinogen receptor.

V. M. Kabanov, Tetiana M. Khristova, A. Varnek, 2011, Bioorganic & medicinal chemistry letters.

Discovery of novel chemical reactions by deep generative recurrent neural network

D. Horvath, A. Varnek, O. Klimchuk, 2020, Scientific Reports.

Virtual screening, synthesis and biological evaluation of DNA intercalating antiviral agents.

Igor A. Levandovskiy, D. Horvath, A. Varnek, 2017, Bioorganic & medicinal chemistry letters.

Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis

Alexandre Varnek, Timur I. Madzhidov, Arkadii I. Lin, 2016, J. Chem. Inf. Model..

Recovery of uranium (VI) from concentrated phosphoric acid by mixtures of new bis(1,3- dialkyloxypropan-2-yl) phosphoric acids and tri-n-octylphosphine oxide

A. Varnek, G. Cote, A. Chagnes, 2013 .

Generative Topographic Mapping Approach to Chemical Space Analysis

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2017 .

The One‐Class Classification Approach to Data Description and to Models Applicability Domain

Igor I Baskin, Alexandre Varnek, Natalia Kireeva, 2010, Molecular informatics.

Chemography: Searching for Hidden Treasures

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2020, J. Chem. Inf. Model..

Evolution of commercially available compounds for HTS.

Alexandre Varnek, Dragos Horvath, Olena Savych, 2019, Drug discovery today.

An Investigation into the Stephens-Castro Synthesis of Dehydrotriaryl[12]annulenes: Factors Influencing the Cyclotrimerization

A. Varnek, S. Cianférani, J. Strub, 2019, European Journal of Organic Chemistry.

Individual Hydrogen‐Bond Strength QSPR Modelling with ISIDA Local Descriptors: a Step Towards Polyfunctional Molecules

Fiorella Ruggiu, Dragos Horvath, Gilles Marcou, 2014, Molecular informatics.

Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2012, J. Chem. Inf. Model..

Molecular dynamics and free energy perturbation studies of Ca2+/Sr2+ complexation selectivities of the macrocyclic ionophores DOTA and TETA in water

A. Varnek, A. Bilyk, G. Wipff, 1999 .

QSPR ensemble modelling of the 1:1 and 1:2 complexation of Co2+, Ni2+, and Cu2+ with organic ligands: relationships between stability constants

Alexandre Varnek, Vitaly P. Solov'ev, Aslan Yu. Tsivadze, 2014, Journal of Computer-Aided Molecular Design.

Synthesis and structure of heterometallic compounds of [RuNO(NO2)4OH]2− with triphenyl phosphine oxide complexes of Co(II), Ni (II), and Zn(II)

A. Varnek, A. Virovets, M. Rohmer, 2007 .

The structure of new heterometallic Ru/M (M=Cu, Ni, Co, Zn) complexes investigated by combined spectroscopic and modeling studies

A. Varnek, V. Kalchenko, G. Wipff, 2002 .

On the nature of the isomer shift in tin(IV) tetrachloride complexes with organic ligands from quantum chemical data

A. Varnek, V. A. Varnek, 1997 .

Assessment of the Macrocyclic Effect for the Complexation of Crown-Ethers with Alkali Cations Using the Substructural Molecular Fragments Method

Alexandre Varnek, Vitaly P. Solov'ev, Georges Wipff, 2002, J. Chem. Inf. Comput. Sci..

Toward in Silico Modeling of Dynamic Combinatorial Libraries

D. Horvath, A. Varnek, G. Marcou, 2022, ACS central science.

New Wide Rim Phosphomethylated Calix[4]arenes in Extraction of Americium and Europium

V. Babain, I. Smirnov, A. Varnek, 2004 .

New organophosphorus calix[4]arene ionophores for trivalent lanthanide and actinide cations

I. Smirnov, A. Varnek, O. Klimchuk, 2002 .

Molecular dynamics study of p-tert-butylcalix[4]arenetetraamide and its complexes with neutral and cationic guests. Influence of solvation on structures and stabilities

A. Varnek, G. Wipff, P. Guilbaud, 1993 .

Solvent and counterion effects on Na+Cs+ complexation selectivity by conformationally locked calix[4]-bis-crown ligands: Molecular Dynamics and Free Energy Perturbation studies in water and methanol, acetonitrile and chloroform solutions

A. Varnek, G. Wipff, 1996 .

MOLECULAR MODELLING IN SOLVENT EXTRACTION : IONOPHORES IN PURE SOLUTIONS AND AT THE LIQUID/LIQUID INTERFACE

A. Varnek, G. Wipff, 1999 .

Calixarenes grafted with Bu2P(O)CH2O binding groups at the narrow rim: synthesis, structure and extraction of heterometallic Ru/Zn complexes

A. Varnek, O. Klimchuk, V. Kalchenko, 2011 .

Upper Rim Thioether Derivatives of Calix[4,6]Arenes: Extraction of Fission Pd(II) and Ag(I)

A. Varnek, V. Kalchenko, G. Wipff, 2005 .

Synthesis and Extractive Properties of Hexaphosphorylated Calix[6]arenes

V. Babain, I. Smirnov, A. Varnek, 2002 .

QSPR ensemble modelling of alkaline-earth metal complexation

A. Varnek, V. Solov'ev, A. Tsivadze, 2013, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

New Approach for Accurate QSPR Modeling of Metal Complexation: Application to Stability Constants of Complexes of Lanthanide Ions Ln 3+ , Ag + , Zn 2+ , Cd 2+ and Hg 2+ with Organic Ligands in Water

Alexandre Varnek, Vitaly P. Solov'ev, A. Yu. Tsivadze, 2012 .

Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores

Igor V. Tetko, Nicolas Lachiche, Frank Hoonakker, 2006, J. Chem. Inf. Model..

Modeling of Ion Complexation and Extraction Using Substructural Molecular Fragments

Alexandre Varnek, Vitaly P. Solov'ev, Georges Wipff, 2000, J. Chem. Inf. Comput. Sci..

Synthesis of a strained acetylenic macrocycle incorporating a para-oligo[2]cruciform bridge bent over nanoscopic dimensions: structural, electronic, spectroscopic, and ion-sensing properties.

A. Varnek, J. Gisselbrecht, P. Baxter, 2013, Chemistry.

Adsorption of Ionophores and of Their Cation Complexes at the Water/Chloroform Interface: A Molecular Dynamics Study of a [2.2.2]Cryptand and of Phosphoryl‐Containing Podands

A. Varnek, L. Troxler, G. Wipff, 1997 .

Complexes of the H5O2+ and H3O+ cations with polyethers in water saturated dichloroethane solutions. A combined IR spectroscopic and quantum mechanics study

A. Varnek, M. Raimondi, G. Wipff, 2002 .

Solvent and Dynamic Effects on the Structure of Alkali Cation Complexes of the t-Butyl-calix[4]arene Anion: MD and FEP Computer Investigations on the Na+/Cs+ Binding Affinity

C. Sirlin, A. Varnek, G. Wipff, 1996 .

An application of the Miertus‐Scrocco‐Tomasi solvation model in molecular mechanics and dynamics simulations

Alexandre Varnek, D. Feil, Georges Wipff, 1995, J. Comput. Chem..

Structure—property modeling of metal binders using molecular fragments

A. Varnek, V. P. Solovev, A. A. Varnek, 2004 .

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

A. Varnek, G. Wipff, A. Collet, 1998 .

MD SIMULATIONS ON IONOPHORES AT A WATER-CHLOROFORM INTERFACE. PART I. CALIX4ARENES UNCOMPLEXED AND THE 222 CRYPTAND

A. Varnek, L. Troxler, G. Wipff, 1996 .

Computer-aided design of new metal binders

A. Varnek, G. Marcou, D. Fourches, 2008 .

Theoretical calculations of extraction selectivity: Alkali cation complexes of calix[4]‐bis‐crown6 in pure water, chloroform, and at a water/chloroform interface

A. Varnek, G. Wipff, A. Varnek, 1996 .

A Direct One‐Pot Synthesis of Asymmetric Dehydrobenzopyrido[12]annulenes and Their Physicochemical Properties

A. Varnek, S. Cianférani, J. Gisselbrecht, 2017 .

Continuous indicator fields: a novel universal type of molecular fields

Igor I. Baskin, Alexandre Varnek, Nelly I. Zhokhova, 2015, Journal of Computer-Aided Molecular Design.

QSAR modeling of blood:air and tissue:air partition coefficients using theoretical descriptors.

Alexandre Varnek, Mati Karelson, Minati Kuanar, 2005, Bioorganic & medicinal chemistry.

Electrochemical properties of substituted 2-methyl-1,4-naphthoquinones: redox behavior predictions.

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2015, Chemistry.

A critical overview of computational approaches employed for COVID-19 drug discovery

Tudor I. Oprea, Rommie E. Amaro, G. Schneider, 2021, Chemical Society reviews.

Visualization of a Multidimensional Descriptor Space

Igor I. Baskin, Héléna A. Gaspar, A. Varnek, 2016 .

Complexation of phosphoryl-containing mono-, bi- and tri-podands with alkali cations in acetonitrile. Structure of the complexes and binding selectivity

Alexandre Varnek, Vitaly P. Solov'ev, Georges Wipff, 1998 .

Unprecedented role of water in self-assembly of potential molecular tweezers

A. Varnek, M. Gross, S. Meyer, 2000 .

Transductive Support Vector Machines: Promising Approach to Model Small and Unbalanced Datasets

Alexandre Varnek, Evgeny Kondratovich, Igor I. Baskin, 2013, Molecular informatics.

Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2016, J. Chem. Inf. Model..

Bagging and Boosting of Classification Models

Igor I. Baskin, Dragos Horvath, Gilles Marcou, 2017 .

Bagging and Boosting of Regression Models

Igor I. Baskin, Dragos Horvath, Gilles Marcou, 2017 .

Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis?

Igor I. Baskin, Alexandre Varnek, A. Varnek, 2012, J. Chem. Inf. Model..

Estimation of the size of drug-like chemical space based on GDB-17 data

Alexandre Varnek, Timur I. Madzhidov, Pavel G. Polishchuk, 2013, Journal of Computer-Aided Molecular Design.

Chemoinformatics-Driven Design of New Physical Solvents for Selective CO2 Absorption.

D. Horvath, A. Varnek, G. Marcou, 2021, Environmental science & technology.

Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints

Igor I. Baskin, Gilles Marcou, Vladimir I. Chupakhin, 2013, J. Chem. Inf. Model..

Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection

Igor V. Tetko, Hao Zhu, Alexandre Varnek, 2008, J. Chem. Inf. Model..

CATMoS: Collaborative Acute Toxicity Modeling Suite

Kimberley M. Zorn, Daniel P. Russo, Timothy E. H. Allen, 2021, Environmental health perspectives.

QSAR without borders.

Artem Cherkasov, Tudor I. Oprea, Jürgen Bajorath, 2020, Chemical Society reviews.

Predicting S. aureus antimicrobial resistance with interpretable genomic space maps

D. Horvath, A. Varnek, G. Marcou, 2023, bioRxiv.

HIV-1 drug resistance profiling using amino acid sequence space cartography

V. Poroikov, D. Horvath, A. Varnek, 2021, bioRxiv.

Multi-task generative topographic mapping in virtual screening

Bernd Beck, Gilles Marcou, Alexandre Varnek, 2019, Journal of Computer-Aided Molecular Design.

GTM‐Based QSAR Models and Their Applicability Domains

Héléna A. Gaspar, I I Baskin, H A Gaspar, 2015, Molecular informatics.

An Evolutionary Optimizer of libsvm Models

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2014 .

Artificial intelligence in synthetic chemistry: achievements and prospects

Igor I. Baskin, Alexandre Varnek, Timur I. Madzhidov, 2017 .

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set

Igor V. Tetko, Artem Cherkasov, Klaus-Robert Müller, 2010, J. Chem. Inf. Model..

Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients

Igor V. Tetko, Igor I. Baskin, Gilles Marcou, 2009, J. Chem. Inf. Model..

A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2021, J. Chem. Inf. Model..

AntiMalarial Mode of Action (AMMA) Database: Data Selection, Verification and Chemical Space Analysis

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2018, Molecular informatics.

Fragment descriptors in structure-property modeling and virtual screening.

Alexandre Varnek, A. Varnek, 2011, Methods in molecular biology.

Prediction of the Glass-Transition Temperatures of Linear Homo/Heteropolymers and Cross-Linked Epoxy Resins

D. Horvath, A. Varnek, G. Marcou, 2019, ACS Applied Polymer Materials.

"Big Data" Fast Chemoinformatics Model to Predict Generalized Born Radius and Solvent Accessibility as a Function of Geometry

Dragos Horvath, Alexandre Varnek, Gilles Gérard Marcou, 2020, J. Chem. Inf. Model..

Serum-based differentiation between multiple sclerosis and amyotrophic lateral sclerosis by Random Forest classification of FTIR spectra.

A. Varnek, G. Marcou, P. Hellwig, 2019, The Analyst.

Fragment Descriptors in SAR/QSAR/QSPR Studies, Molecular Similarity Analysis and in Virtual Screening

A. Varnek, I. Baskin, 2009 .

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

Ruili Huang, Scott Boyer, Xin Hu, 2020, Environmental health perspectives.

Comprehensive Analysis of Applicability Domains of QSPR Models for Chemical Reactions

Alexandre Varnek, Igor I Baskin, Timur I Madzhidov, 2020, International journal of molecular sciences.

Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis

Alexandre Varnek, Victor Kuzmin, Liudmila Ognichenko, 2016, J. Chem. Inf. Model..

Synthesis, biological evaluation, X-ray molecular structure and molecular docking studies of RGD mimetics containing 6-amino-2,3-dihydroisoindolin-1-one fragment as ligands of integrin αIIbβ₃.

V. M. Kabanov, Tetiana M. Khristova, A. Varnek, 2013, Bioorganic & medicinal chemistry.

Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points?

Igor V. Tetko, Igor I. Baskin, Alexandre Varnek, 2007, J. Chem. Inf. Model..

Predicting the Predictability: A Unified Approach to the Applicability Domain Problem of QSAR Models

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2009, J. Chem. Inf. Model..

Pros and cons of virtual screening based on public "Big Data": In silico mining for new bromodomain inhibitors.

Jürgen Bajorath, Dragos Horvath, Alexandre Varnek, 2019, European journal of medicinal chemistry.

Prediction of Optimal Conditions of Hydrogenation Reaction Using the Likelihood Ranking Approach

A. Varnek, V. Afonina, V. Burilov, 2021, International journal of molecular sciences.

Expert System for Predicting Reaction Conditions: The Michael Reaction Case

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2015, J. Chem. Inf. Model..

Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures

Alexandre Varnek, Frank Hoonakker, Denis Fourches, 2005, J. Comput. Aided Mol. Des..

QSPR Modeling of the AmIII/EuIII Separation Factor: How Far Can we Predict ?

Alexandre Varnek, Denis Fourches, Vitaly P. Solov'ev, 2007 .

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

Igor V. Tetko, Hao Zhu, Artem Cherkasov, 2008, J. Chem. Inf. Model..

SOLVENT EXTRACTION OF METAL PICRATES BY PHOSPHORYL-CONTAINING PODANDS

J. D. Lamb, A. Varnek, G. Wipff, 1999 .

Rapid Discrimination of Neuromyelitis Optica Spectrum Disorder and Multiple Sclerosis Using Machine Learning on Infrared Spectra of Sera

A. Varnek, G. Marcou, P. Hellwig, 2022, International journal of molecular sciences.

Generative Topographic Mapping Approach to Modeling and Chemical Space Visualization of Human Intestinal Transporters

A. Varnek, G. Marcou, T. Madzhidov, 2016, BioNanoScience.

Chemoinformatics as a Theoretical Chemistry Discipline

Igor I Baskin, Alexandre Varnek, A. Varnek, 2011, Molecular informatics.

Supramolecular Chemistry: Computer-Assisted Instruction in Undergraduate and Graduate Chemistry Courses

A. Varnek, J. Lehn, E. Boldyreva, 2000 .

NP Navigator: A New Look at the Natural Product Chemical Space

P. Ertl, D. Horvath, A. Varnek, 2021, Molecular informatics.

Parallel Generative Topographic Mapping: An Efficient Approach for Big Data Handling

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2020, Molecular informatics.

De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping

Dragos Horvath, Gilles Marcou, Igor I Baskin, 2019, J. Chem. Inf. Model..

Chemical Data Visualization and Analysis with Incremental Generative Topographic Mapping: Big Data Challenge

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2015, J. Chem. Inf. Model..

Chapter 1:Fragment Descriptors in SAR/QSAR/QSPR Studies, Molecular Similarity Analysis and in Virtual Screening

Igor I. Baskin, Alexandre Varnek, A. Varnek, 2008 .

Computational chemogenomics: Is it more than inductive transfer?

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2014, Journal of Computer-Aided Molecular Design.

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

Igor V. Tetko, Antony J. Williams, Artem Cherkasov, 2011, J. Comput. Aided Mol. Des..

Prediction of Activity Cliffs Using Condensed Graphs of Reaction Representations, Descriptor Recombination, Support Vector Machine Classification, and Support Vector Regression

Jürgen Bajorath, Gilles Marcou, Alexandre Varnek, 2016, J. Chem. Inf. Model..

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

Igor V. Tetko, Antony J. Williams, Artem Cherkasov, 2011, Journal of Cheminformatics.

Computational screening methodology identifies effective solvents for CO2 capture

D. Horvath, A. Varnek, G. Marcou, 2022, Communications Chemistry.

Computer-Aided Design of New Physical Solvents for Hydrogen Sulfide Absorption

D. Horvath, A. Varnek, G. Marcou, 2021 .

Correction: QSAR without borders.

Tudor I. Oprea, I. Tetko, D. Agrafiotis, 2020, Chemical Society reviews.

Machine learning modelling of chemical reaction characteristics: yesterday, today, tomorrow

A. Varnek, V. Afonina, I. Baskin, 2021, Mendeleev Communications.

Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS)

Alban Arrault, Philippe Vayer, Dragos Horvath, 2013, J. Chem. Inf. Model..

SynthI: A New Open-Source Tool for Synthon-Based Library Design

D. Horvath, A. Varnek, O. Klimchuk, 2021, J. Chem. Inf. Model..

Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery

A. Varnek, D. Osolodkin, A. Egorov, 2021, Frontiers in Pharmacology.

Rescoring of docking poses under Occam’s Razor: are there simpler solutions?

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2018, Journal of Computer-Aided Molecular Design.

CovaDOTS: In Silico Chemistry-Driven Tool to Design Covalent Inhibitors Using a Linking Strategy

Dragos Horvath, Alexandre Varnek, Philippe Roche, 2019, J. Chem. Inf. Model..

Modern Trends in Chemical Reactions Modeling

A. Varnek, I. Baskin, 2021, Systems Medicine.

Cross-validation strategies in QSPR modelling of chemical reactions

A. Varnek, I. Baskin, T. Madzhidov, 2021, SAR and QSAR in environmental research.

Virtual Screening with Generative Topographic Maps: How Many Maps Are Required?

Jürgen Bajorath, Dragos Horvath, Gilles Marcou, 2018, J. Chem. Inf. Model..

"In Silico" Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands: QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests

Dan C. Fara, Alexandre Varnek, Alan R. Katritzky, 2004, J. Chem. Inf. Model..

Predictive Models for Halogen‐bond Basicity of Binding Sites of Polyfunctional Molecules

Marta Glavatskikh, Dragos Horvath, Gilles Marcou, 2016, Molecular informatics.

Predictive cartography of metal binders using generative topographic mapping

Igor I. Baskin, Alexandre Varnek, Vitaly P. Solov'ev, 2017, Journal of Computer-Aided Molecular Design.

Quantitative Structure—Property Relationships in Solvent Extraction and Complexation of Metals

A. Varnek, V. Solov'ev, 2010 .

Stochastic versus Stepwise Strategies for Quantitative Structure-Activity Relationship GenerationHow Much Effort May the Mining for Successful QSAR Models Take?

Alexandre Varnek, Dragos Horvath, Fanny Bonachéra, 2007, J. Chem. Inf. Model..

"In silico" design of potential anti-HIV actives using fragment descriptors.

A Varnek, A. Varnek, V. Solov'ev, 2005, Combinatorial chemistry & high throughput screening.

Quantitative Structure-Property Relationship Modeling of beta-Cyclodextrin Complexation Free Energies

Dan C. Fara, Hongfang Yang, Takahiro Suzuki, 2004, J. Chem. Inf. Model..

Endocrine disruption: the noise in available data adversely impacts the models’ performance

E. Van Miert, A. Varnek, G. Marcou, 2021, SAR and QSAR in environmental research (Print).

Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2015, Journal of Computer-Aided Molecular Design.

Modelling of ready biodegradability based on combined public and industrial data sources

G Marcou, F Lunghini, P Gantzer, 2019, SAR and QSAR in environmental research.

Prediction of drug induced liver injury using molecular and biological descriptors.

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2015, Combinatorial chemistry & high throughput screening.

Exploration of the Chemical Space of DNA‐encoded Libraries

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2021, Molecular informatics.

SynthI: a new open-source tool for synthon-based library design

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2021 .

Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2016, J. Chem. Inf. Model..

Investigation of hydration effects of dibenzodialkyl-18-crown-6 complexes with the potassium ion by the Monte-Carlo method

V. Kukhar, A. Varnek, V. E. Khutorskii, 1990 .

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

Igor V. Tetko, Artem Cherkasov, Paola Gramatica, 2008, Journal of Chemical Information and Modeling.

Implementation of a soft grading system for chemistry in a Moodle plugin

A. Varnek, G. Marcou, R. Schurhammer, 2022, Journal of Cheminformatics.

S4MPLE—Sampler for Multiple Protein-Ligand Entities: Methodology and Rigid-Site Docking Benchmarking

Dragos Horvath, Gilles Marcou, Camelia Chira, 2015, Molecules.

QSPR models for bioconcentration factor (BCF): are they able to predict data of industrial interest?

G Marcou, R Patoux, F Lunghini, 2019, SAR and QSAR in environmental research.

QSAR modeling and chemical space analysis of antimalarial compounds

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2017, Journal of Computer-Aided Molecular Design.

Challenges for Kinetics Predictions via Neural Network Potentials: A Wilkinson’s Catalyst Case

A. Varnek, Yu Harabuchi, Ruben Staub, 2023, Molecules.

Chemoinformatics approaches to virtual screening

Alexandre Varnek, A. Tropsha, A. Varnek, 2008 .

Structure–reactivity modeling using mixture-based representation of chemical reactions

Alexandre Varnek, Timur I. Madzhidov, Pavel G. Polishchuk, 2017, Journal of Computer-Aided Molecular Design.

Inverse QSAR: Reversing Descriptor-Driven Prediction Pipeline Using Attention-Based Conditional Variational Autoencoder

Arkadii I. Lin, D. Horvath, A. Varnek, 2022, J. Chem. Inf. Model..

CGRtools: Python Library for Molecule, Reaction, and Condensed Graph of Reaction Processing

Alexandre Varnek, Timur I Madzhidov, Ramil I Nugmanov, 2019, J. Chem. Inf. Model..

Skin permeation rate as a function of chemical structure.

Alexandre Varnek, Mati Karelson, Kaido Tämm, 2006, Journal of medicinal chemistry.

GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design.

D. Horvath, A. Varnek, G. Marcou, 2023, Journal of Chemical Information and Modeling.

Interpretability of SAR/QSAR Models of any Complexity by Atomic Contributions

D Horvath, G Marcou, A Varnek, 2012, Molecular informatics.

Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite

Stephen P. Boyd, Kimberley M. Zorn, Daniel P. Russo, 2021, Environmental health perspectives.

Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, Structure‐Activity Modeling and Dataset Comparison

Héléna A. Gaspar, N Kireeva, I I Baskin, 2012, Molecular informatics.

Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data

A. Varnek, S. Maeda, Pavel Sidorov, 2020, Journal of Chemical Information and Modeling.

Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery

D. Horvath, A. Varnek, O. Klimchuk, 2022, J. Chem. Inf. Model..

CGRdb2.0: A Python Database Management System for Molecules, Reactions, and Chemical Data

A. Varnek, Pavel Sidorov, T. Madzhidov, 2021, J. Chem. Inf. Model..

A Representation to Apply Usual Data Mining Techniques to Chemical reactions - Illustration on the Rate Constant of SN2 reactions in water

Nicolas Lachiche, Frank Hoonakker, Alexandre Varnek, 2010, Int. J. Artif. Intell. Tools.

Prediction of Tautomer Equilibrium Constants Using Condensed Graphs of Reaction

A. Varnek, I. Baskin, I. Antipin, 2015 .

Transductive Support Vector Machines: Promising Approach to Model Small and Unbalanced Datasets

A. Varnek, I. Baskin, E. Kondratovich, 2013, Molecular Informatics.

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

I. Tetko, A. Tropsha, Phuong Dao, 2008, J. Chem. Inf. Model..

Transductive Ridge Regression in Structure‐activity Modeling

Nicolas Lachiche, Dragos Horvath, Gilles Marcou, 2018, Molecular informatics.

Building a chemical space based on fragment descriptors.

Alexandre Varnek, Igor Baskin, A. Varnek, 2008, Combinatorial chemistry & high throughput screening.

Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis

A. Varnek, O. Tinkov, P. Polishchuk, 2016, J. Chem. Inf. Model..

From bird’s eye views to molecular communities: two-layered visualization of structure–activity relationships in large compound data sets

Jürgen Bajorath, Alexandre Varnek, Dragos Horvath, 2017, Journal of Computer-Aided Molecular Design.

Chemical Data Visualization and Analysis with Incremental Generative Topographic Mapping: Big Data Challenge

Héléna A. Gaspar, D. Horvath, A. Varnek, 2015, J. Chem. Inf. Model..

Complexation of lithium and sodium cations with β-phosphorylate ethers, modelling terminal groups of organophosphorus podands. An experimental and theoretical study

A. Varnek, V. Solov'ev, J. E. Elshof, 1992 .

Prediction of Optimal Salinities for Surfactant Formulations Using a Quantitative Structure-Property Relationships Approach

A. Varnek, B. Creton, A. Maldonado, 2015 .

Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points?

I. Tetko, A. Varnek, V. Solov'ev, 2007, J. Chem. Inf. Model..

Serum-based differentiation between multiple sclerosis and amyotrophic lateral sclerosis by Random Forest classification of FTIR spectra.

A. Varnek, G. Marcou, P. Hellwig, 2019, The Analyst.

Sydnone-alkyne cycloaddition: Which factors are responsible for reaction rate ?

A. Varnek, O. Klimchuk, T. Madzhidov, 2019 .

Meta-GTM: Visualization and Analysis of the Chemical Library Space

D. Horvath, A. Varnek, G. Marcou, 2023, J. Chem. Inf. Model..

Chemical Library Space: Definition and DNA-Encoded Library Comparison Study Case

D. Horvath, A. Varnek, G. Marcou, 2023, J. Chem. Inf. Model..

The chemical library space and its application to DNA-Encoded Libraries

D. Horvath, A. Varnek, G. Marcou, 2023 .

Design, Virtual Screening, and Synthesis of Antagonists of αIIbβ3 as Antiplatelet Agents.

V. M. Kabanov, Tetiana M. Khristova, T. Langer, 2015, Journal of Medicinal Chemistry.

Trustworthiness, the Key to Grid-Based Map-Driven Predictive Model Enhancement and Applicability Domain Control

D. Horvath, A. Varnek, G. Marcou, 2020, J. Chem. Inf. Model..

Do Not Hesitate to Use Tversky - and Other Hints for Successful Active Analogue Searches with Feature Count Descriptors

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2013, J. Chem. Inf. Model..

Local neighborhood behavior in a combinatorial library context

Gilles Marcou, Gisbert Schneider, Alexandre Varnek, 2011, J. Comput. Aided Mol. Des..

Correlation of blood-brain penetration using structural descriptors.

Alexandre Varnek, Mati Karelson, Minati Kuanar, 2006, Bioorganic & medicinal chemistry.

Predicting Highly Enantioselective Catalysts Using Tunable Fragment Descriptors.

A. Varnek, Pavel Sidorov, T. Gimadiev, 2023, Angewandte Chemie.

Visualization and Analysis of the REACH‐chemical Space with Generative Topographic Mapping

Alexandre Varnek, Philippe Azam, Filippo Lunghini, 2020, Molecular informatics.

Reaction Data Curation I: Chemical Structures and Transformations Standardization

Arkadii I. Lin, H. Ceulemans, A. Varnek, 2021, Molecular informatics.

of the BIGCHEM Session

Arkadii I. Lin, O. Engkvist, D. Horvath, 2019 .

QSPR modelling -a valuable support in HTS quality control

Fiorella Ruggiu, Patrick Gizzi, Jean-Luc Galzi, 2014 .