Alexandre Varnek

发表

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, 2011, Int. J. Artif. Intell. Tools.

Diversifying chemical libraries with generative topographic mapping

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2019, Journal of Computer-Aided Molecular Design.

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.

Chemical space: design, visualization and navigation

Alexandre Varnek, 2012 .

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

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

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.

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.

QSAR modeling and chemical space analysis of antimalarial compounds

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

Generative Topographic Mapping of Conformational Space

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2017, 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..

Relational Chemical Databases

Gilles Marcou, Alexandre Varnek, 2017 .

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..

"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..

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

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

Stargate GTM: Bridging Descriptor and Activity Spaces

Igor I. Baskin, Gilles Marcou, Alexandre Varnek, 2015, J. Chem. Inf. Model..

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..

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..

Cross-Validation and the Variable Selection Bias

Igor I. Baskin, Gilles Marcou, Alexandre Varnek, 2017 .

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..

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

Gilles Marcou, Alexandre Varnek, Timur I. Madzhidov, 2016 .

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..

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

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

Fragment Descriptors in Virtual Screening

Igor I. Baskin, Alexandre Varnek, 2013 .

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

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

Transductive Ridge Regression in Structure‐activity Modeling

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

Assessment of tautomer distribution using the condensed reaction graph approach

Igor I. Baskin, Alexandre Varnek, Timur I. Madzhidov, 2018, Journal of Computer-Aided Molecular Design.

Generative Topographic Mapping Approach to Chemical Space Analysis

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2017 .

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..

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.

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..

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..

Benchmarking Machine‐Learning Methods

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

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

Jürgen Bajorath, Dragos Horvath, Gilles Marcou, 2018, 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..

Handling of Markush Structures

Alexandre Varnek, Timur I. Madzhidov, R. I. Nugmanov, 2017 .

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.

Generative Topographic Mapping of the Docking Conformational Space

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2019, Molecules.

Local neighborhood behavior in a combinatorial library context

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

Tutorials in Chemoinformatics

Alexandre Varnek, 2017 .

Evolution of commercially available compounds for HTS.

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

Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps

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

ISIDA Fragmentor2015 - User Manual

Fiorella Ruggiu, Alexandre Varnek, Dragos Horvath, 2015 .

Random Subspaces and Random Forest

Igor I. Baskin, Gilles Marcou, Alexandre Varnek, 2017 .

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, 1996, J. Comput. Chem..

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

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

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.

A unified approach to the applicability domain problem of QSAR models

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2010, J. Cheminformatics.

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.

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..

A Summer School for Structuring the Chemoinformatics Community

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

Multi-task generative topographic mapping in virtual screening

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

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

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

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

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

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..

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.

A fast and Space-Efficient boundary element method for computing electrostatic and hydration effects in large molecules

Alexandre Varnek, Randy J. Zauhar, 1996, J. Comput. Chem..

Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset

Nicolas Lachiche, Gilles Marcou, Alexandre Varnek, 2010, J. Cheminformatics.

Bagging and Boosting of Classification Models

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

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

Dan C. Fara, Hongfang Yang, Takahiro Suzuki, 2004, 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..

An Evolutionary Optimizer of libsvm Models

Gilles Marcou, Alexandre Varnek, Dragos Horvath, 2014 .

Fragment descriptors in structure-property modeling and virtual screening.

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

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..

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

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

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..

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, Georges Wipff, Severine Helissen, 1998, J. Comput. Chem..

Bagging and Boosting of Regression Models

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

Computational chemogenomics: Is it more than inductive transfer?

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

Chemoinformatics as a Theoretical Chemistry Discipline

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

Building a chemical space based on fragment descriptors.

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

Instability of Interpretable Rules

Igor I. Baskin, Gilles Marcou, Alexandre Varnek, 2017 .

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..

AUTOMATIC SYSTEM FOR PREDICTION OF OPTIMAL CONDITION FOR HYDROGENATION REACTIONS

Alexandre Varnek, Timur I. Madzhidov, R. I. Nugmanov, 2017 .

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..

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

Alexandre Varnek, Vitaly P. Solov'ev, 2003, J. Chem. Inf. Comput. Sci..

Chemography: Searching for Hidden Treasures

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

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

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2021 .

Exploration of the Chemical Space of DNA‐encoded Libraries

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

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..

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

Igor I. Baskin, Alexandre Varnek, Timur I. Madzhidov, 2021, J. Chem. Inf. Model..

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

Alexandre Varnek, Timur I. Madzhidov, Satoshi Maeda, 2021, J. Chem. Inf. Model..

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

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

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

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

ehp CERAPP : Collaborative Estrogen Receptor Activity Prediction Project

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

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

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

TOWARDS AN INFORMATION SYSTEM ON SOLVENT EXTRACTION

Alexandre Varnek, Vitaly P. Solov'ev, Georges Wipff, 2001 .

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

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

Monitoring of the Conformational Space of Dipeptides by Generative Topographic Mapping

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

Using self-organizing maps to accelerate similarity search.

Dragos Horvath, Gilles Marcou, Alexandre Varnek, 2012, Bioorganic & medicinal chemistry.

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

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

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

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

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.

Alexandre Varnek, Vitaly P. Solov'ev, 2003 .

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

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

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 .

Chemoinformatics approaches to virtual screening

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

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

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

Correlation of blood-brain penetration using structural descriptors.

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

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

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

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

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

Quantitative Structure—Property Relationship Modeling of β-Cyclodextrin Complexation Free Energies.

Dan C. Fara, Hongfang Yang, Takahiro Suzuki, 2004 .

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

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

Combinatorial QSAR Modeling of Chemical Toxicants Tested Against Tetrahymena pyriformis.

Igor V. Tetko, Artem Cherkasov, Paola Gramatica, 2008 .

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.

Skin permeation rate as a function of chemical structure.

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

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.

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 .