Publications

Paul N. W. Baxter, Abdelaziz Al-Ouahabi, Jean-Paul Gisselbrecht, Lydia Brelot, André De Cian, Alexandre Varnek
Electronic, Spectroscopic, Ion-Binding and Structural Property Screening of a Dehydro[m]pyrido[n]annulene Library : A Strategy for the Discovery of Optimal Candidates for Supramolecular Materials Engineering.
J. Org. Chem, 2012, 77 (1), 126–142

N. Kireeva, I.I. Baskin, H. A. Gaspar a, D. Horvath, G. Marcou and A. Varnek
Generative Topographic Maps (GTM) : universal tool for data visualization, structure-activity modeling and database comparison.
Mol. Informatics, 2012, 31, 201-312

Fanny Bonachera, ; Gilles Marcou, ; Natalia Kireeva, Alexandre Varnek, Dragos Horvath
Using Self-Organizing Maps to Accelerate Similarity Search
Bioorg Med Chem, 2012 Apr 21

Alexandre Varnek and Igor Baskin
Machine Learning Methods for Property Prediction in Chemoinformatics : Quo Vadis ?
J. Chem. Inf. Model. 2012, 52, 1413−1437

Oprisiu, E. Varlamova, E. Muratov, A. Artemenko, G. Marcou, P. Polishchuk, V. Kuz’min, A. Varnek
QSPR approaches to predict non-additive properties of mixtures. Application to bubble point temperatures of binary mixtures of liquids.
Mol. Informatics, 2012, 31, 491 – 502

G. Marcou, D. Horvath, V. Solov’ev, A. Arrault, P. Vayer, A. Varnek
Interpretability of SAR/QSAR models of any complexity by atomic contributions
Mol. Informatics, 2012, accepted

V. P. Solov’ev, N. Kireeva, A. Yu. Tsivadze and A. Varnek,
QSPR Consensus Models for Alkaline-Earth Metal Complexation
J. Inclusion Phenomena and Macrocyclic Chemistry, DOI 10.1007/s10847-012-0185-x

Aurélie de Luca, Dragos Horvath, Gilles Marcou, Vitaly P. Solov’ev and Alexandre Varnek
Neighborhood Behavior and Clustering of Chemical Reactions using Condensed Graphs of Reactions approach.
J. Chem. Inf. Model. 2012, accepted

Torgov V.G., Kostin G.A, Us T.V., Korda T.M., Klimchuk O.V., Miroshnichenko S.I., Suwinska K., Varnek A.A., Kalchenko V. I.
Calixarenes grafted with Bu2P(O)CH2O binding groups at the narrow rim. Synthesis, structure and extraction of heterometallic Ru/Zn complexes.
J. Inclusion Phenomena and Macrocyclic Chemistry, 2011, 71 (1), 67-77

Alexandre Varnek and Igor I. Baskin
Chemoinformatics as a theoretical chemistry discipline.
Mol. Informatics, 2011, 30, 20 – 32

Christian Koch, Gisbert Schneider, Gilles Marcou, Alexandre Varnek, Dragos Horvath
Local Neighborhood Behavior : Study of a Combinatorial Library Context
J. Computer-Aided Molecular Design, 2011, 25:237–252

Iurii Sushko, Anil Kumar Pandey, Sergii Novotarskyi, Robert Körner, Matthias Rupp,Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Y. Tanchuk, Roberto Todeschini, Alexander Varnek Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria Grishina, Johann Gasteiger, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav Kholodovych, Dmitriy Chekmarev Artem Cherkasov, Joao Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Igor V. Tetko
Online Chemical Modeling Environment (OCHEM) : Web Platform for Data Storage, Model Development and Publishing of Chemical Information
J. Computer-Aided Molecular Design, 2011, 25 (6), 533-54.

Frank Hoonakker, Nicolas Lachiche, Alexandre Varnek and Alain Wagner
Condensed Graph of Reaction : considering a chemical reaction as one single pseudo molecule
International Journal on Artificial Intelligence Tools, 2011, 20, (2), 253-270

Andrei A. Krysko, Georgiy V. Samoylenko, Pavel G. Polishchuk, Sergei A. Andronati, Tatyana A. Kabanova, Tetiana M. Khristova, Victor E. Kuz’min, Vladimir M. Kabanov, Olga L. Krysko, Alexandre A. Varnek and Ruslan Ya. Grygorash
RGD mimetics containing phthalimidine fragment, novel ligands of fibrinogen receptor.
Bioorganic & Medicinal Chemistry Letters, 2011, 21, 5971–5974

Vitaly P. Solov’ev, Ioana Oprisiu, Gilles Marcou and Alexandre Varnek
QSPR Modeling of Normal Boiling Point Temperature and Composition of Binary Azeotropes
Industrial & Engineering Chemistry Research, 2011, 50 (24), 14162–14167

Vitaly P. Solov’ev, Igor V. Sukhno, Vladimir Yu. Buzko, Aleksey A. Polushin, Gilles Marcou, Aslan Yu. Tsivadze, Alexandre Varnek
QSPR modeling of stability constants of the complexes of Zn2+, Cd2+, and Hg2+ with organic ligands in water
J. Inclusion Phenomena and Macrocyclic Chemistry, 2012, 72, 309-321

Frank Hoonakker, Nicolas Lachiche, Alexandre Varnek and Alain Wagner
A representation to apply usual data mining techniques to chemical reactions.
Trends in Applied Intelligent Systems (IEA/AIE’10), 2010, 6097, 318-326.

Igor I. Baskin, Natalia Kireeva and Alexandre Varnek
The One-Class Classification Approach to Data Description and to Models Applicability Domain.
Mol. Informatics, 2010, 581-587

Frank Hoonakker, Nicolas Lachiche, Alexandre Varnek and Alain Wagner
Condensed Graph of Reaction : considering a chemical reaction as one single pseudo molecule
Proceedings of the 19th International Conference on Inductive Logic Programming (ILP’09).

Iurii Sushko, Sergii Novotarskyi, Robert Korner, Anil Kumar Pandey, Jiazhong Li, Paola Gramatica, Katja Hansen, Timon Schroeter, Klaus-Robert Muller, Lili Xi, Huanxiang Liu, Xiaojun Yao, Tomas Oberg, Artem Cherkasov, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Roberto Todeschini, Denis Fourches, Eugene Muratov, Alexander Tropsha, Igor Baskin, Dragos Horvath, Gilles Marcou, Christophe Muller, Alexander Varnek, Volodymyr V. Prokopenko, and Igor V. Tetko
Applicability domains for classification problems : benchmarking of distance to models for AMES mutagenicity set.
J. Chem. Inf. Model. , 2010, 50 (12), 2094–2111

Fiorella Ruggiu, Gilles Marcou, Alexandre Varnek and Dragos Horvath
ISIDA Property-labeled fragment descriptors
Mol. Informatics, 2010, 29, 855 – 868

Gilles Marcou, Isabelle Billard, Ali Ouadi and Alexandre Varnek
In silico design of new ionic liquids (ILs) based on QSPR models of ILs viscosity
J. Phys. Chem. B, 2010, 115 (1), 93–98

G Marcou, N Lachiche, L Brillet, J-M Paris and A Varnek
Learning antibacterial activity against S. Aureus on the Chimiothèque Nationale dataset
Journal of Cheminformatics, 2010, Volume 2, Supplement 1, P30

Gozalbes R, Barbosa F, Nicolai E, Horvath D, Froloff N
Development and Validation of a Pharmacophore-Based QSAR Model for the Prediction of CNS Activity
CHEMMEDCHEM, 4(2), 204-209, 2009

Varnek A, Gaudin C, Marcou G, Baskin I, Pandey AK, Tetko IV,
Inductive Transfer of Knowledge : Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49(1), 133-144, 2009

Varnek A, Fourches D, Kireeva N, Klimchuk O, Marcou G, Tsivadze A, Solov’ev V
Computer-aided design of new metal binders
RADIOCHIMICA ACTA, 96(8), 505-511, 2008

Barillari C, Marcou G, Rognan D
Hot-spots-guided receptor-based pharmacophores (HS-Pharm) : A knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48(7), 1396-1410, 2008

Docking and biomolecular simulations on computer grids : Status and trends
Tantar AA, Conilleau S, Parent B, Melab N, Brillet L, Roy S, Talbi EG, Horvath D
CURRENT COMPUTER-AIDED DRUG DESIGN, 4(3), 235-249, 2008

Bonachera F, Horvath D
Fuzzy tricentric pharmacophore fingerprints. 2. application of topological fuzzy pharmacophore triplets in quantitative structure-activity relationships
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48(2), 409-425, 2008

Podlipnik C, Velter I, La Ferla B, Marcou G, Belvisi L, Nicotra F, Bernardi A
First round of a focused library of cholera toxin inhibitors Record contains structures
CARBOHYDRATE RESEARCH, 342(12-13), 1651-1660, 2007

Marcou G, Rognan D
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 47(1), 195-207, 2007

Hanoulle X, Melchior A, Sibille N, Parent B, Denys A, Wieruszeski JM, Horvath D, Allain F, Lippens G, Landrieu I
Structural and functional characterization of the interaction between cyclophilin B and a heparin-derived oligosaccharide
JOURNAL OF BIOLOGICAL CHEMISTRY, 282(47), 34148-34158, 2007

Parent B, Kokosy A, Horvath D
Optimized evolutionary strategies in conformational sampling
SOFT COMPUTING, 11(1), 63-79, 2007

Mari S, Canada FJ, Jimenez-Barbero J, Bernardi A, Marcou G, Motto I, Velter I, Nicotra F, La Ferla B
Synthesis and conformational analysis of galactose-derived bicyclic scaffolds Record contains structures
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, 13, 2925-2933, 2006

A. R. Katritzky, D.A. Dobchev, D. C. Fara, E. Hür, K. Tämm, L. Kurunczi, M. Karelson, V. P. Solov’ev, A. Varnek
Skin Permeation Rate as a Function of Chemical Structure.
J. Med. Chem, 2006, 49, 3305-3314.

Igor V. Tetko, Vitaly P. Solov’ev, Alexey V. Antonov, Xiaojun Yao, Jean Pierre Doucet, Botao Fan, Frank Hoonakker, Denis Fourches, Pierre Jost, Nicolas Lachiche and Alexandre Varnek
Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores
J. Chem. Inf. Model, 2006, 46(2), 808-819.

V. P. Solov’ev, N.V. Kireeva, A.Yu. Tsivadze, A. A. Varnek
Structure – property modelling of complexation of strontium cation by organic ligands
J. Struct. Chem., 2006, 47, 311-325.

Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes
Bonachera F, Parent B, Barbosa F, Froloff N, Horvath D
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46(6), 2457-2477, 2006

V. Torgov, G. Kostin, T. Korda, E. Stoyanov, V. Kalchenko, A. Drapailo, O. Kasyan, G. Wipff, A. Varnek
Upper rim thioether derivatives of calix[4,6]arenes : synthesis and extraction of fission Pd(II) and Ag(I)
J. Solv. Extr. Ion Exch., 2005, 23(6), 781-801.

A. R. Katritzky, M. Kuanar, D. C. Fara, M. Karelson, W. E. Acree, Jr., V. P. Solov’ev, A. Varnek
QSAR Modeling of Blood:Air and Tissue:Air Partition Coefficients Using Theoretical Descriptors
Bio-organic Medicinal Chemistry, 2005, 13(23), 6450-6463.

A. Varnek, D. Fourches, F. Hoonakker, V. P. Solov’ev
Substructural fragments : an universal language to encode reactions, molecular and supramolecular structures
J. Computer-Aided Molecular Design, 2005, 19, 693-703.

Rolland C, Gozalbes R, Nicolai E, Paugam MF, Coussy L, Barbosa F, Horvath D, Revah F
G-protein-coupled receptor affinity prediction based on the use of a profiling dataset : QSAR design, synthesis, and experimental validation
JOURNAL OF MEDICINAL CHEMISTRY, 48(21), 6563-6574, 2005

Gozalbes R, Rolland C, Nicolai E, Paugam MF, Coussy L, Horvath D, Barbosa F, Mao B, Revah F, Froloff N
QSAR strategy and experimental validation for the development of a GPCR focused library
QSAR & COMBINATORIAL SCIENCE, 24(4), 508-516, 200

V. P. Solov’ev, A. Varnek
Structure – property modeling of metal binders using molecular fragments.
Russian Chem. Bulletin, 2004, 56(7), 1380-1391

A.Varnek, D.Fourches, V.Solov’ev, D.Fara, A.Turanov, A.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. Comp. Sci., 2004, 44, 1365-1382

O. Klimchuk, L. Atamas, S. Miroshnichenko, V. Kalchenko, I. Smirnov, V. Babain, A. Varnek, G. Wipff
New wide rim phosphomethylated calix[4]arenes in extraction of actinides and lanthanides
J. Inclusion Phenom. Macrocyclic Chem., 49, 47-56

Alan R. Katritzky, Dan C. Fara, Hongfang Yang, Mati Karelson, Takahiro Suzuki, Vitaly P. Solov’e, Alexandre Varnek
QSPR Modeling of b - Cyclodextrin Complexation Free Energies
J. Chem. Inf. Comp. Sci., 2004, 44, 529-541

Mao B, Gozalbes R, Barbosa F, Migeon J, Rogalski S, Kamm K, Wong E, Costales C, Shi W, Froloff N, Horvath D, Wu C
Modelling cytochrome P450 inhibition using large datasets of in vitro assays for CYP 2D6 and CYP 3A4
DRUG METABOLISM REVIEWS, 36, 343-343, 2004

Barbosa F, Horvath D
Molecular similarity and property similarity
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 4(6), 589-600, 2004

V. P. Solov’ev, A. 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. Comp. Sci., 2003, 43 , 1703 – 1719

Migeon JC, Rogalski SL, Krejsa CM, Horvath D, Mao B, Barbosa F, Merrick SE, Mersberg M, Lakehal F
Using large in vitro ADME data sets to predict in vivo properties
DRUG METABOLISM REVIEWS, 35, 168-168, 2003

Krejsa CM, Horvath D, Rogalski SL, Penzotti JE, Mao B, Barbosa F, Migeon JC
Predicting ADME properties and side effects : The BioPrint approach
CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT, 6(4), 470-480, 2003

Horvath D, Mao B
Neighborhood behavior. Fuzzy molecular descriptors and their influence on the relationship between structural similarity and property similarity
QSAR & COMBINATORIAL SCIENCE, 22(5), 498-509, 2003

Horvath D, Jeandenans C
Neighborhood behavior of in silico structural spaces with respect to in vitro activity spaces - A novel understanding of the molecular similarity principle in the context of multiple receptor binding profiles
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 43(2), 680-690, 2003

Horvath D, Jeandenans C
Neighborhood Behavior of in silico structural spaces with respect to in vitro activity spaces - A benchmark for Neighborhood Behavior assessment of different in silico similarity metrics
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 43(2), 691-698, 2003

Yu.Rudzevich, A. Drapaylo, V.Rudzevich, V. Miroshnichenko, V.Kalchenko, I. Smirnov, V. Babain, A.Varnek, G.Wipff,
Synthesis and extraction properties of hexaphosphorilated calix[6]arenes.
Russian J. General Chemistry, 2002, 72 , 1840-1846

A. Varnek, B. Dietrich, G. Wipff, J.-M. Lehn, E. V. Boldyreva,
Initiation à la Chimie Supramoléculaire assistée par Ordinateur.
Technique de l’Ingénieur, 2002, AF 6 048-1 - AF 6 048-8

A. Varnek , G. Wipff, V. P. Solov’ev
Towards "in silico" design of new potential extractants using chemical informatics methods.
International Solvent Extraction Conference, Cape Town, South Africa, Mar. 17-21, 2002, 481-486. South African Institute of Mining and Metallurgy, Marshalltown, S. Africa

A. Varnek , G. Wipff, V. P. Solov’ev
Assessment of the macrocyclic effect for the complexation of crown-ethers with alkali cations using Substructural Molecular Fragments.
J. Chem. Inf. Comp. Sci., 2002, 42 , 812-829 .

A. Varnek , G. Wipff, A. Famulari, M. Raimondi, T. Vorobieva, E. Stoyanov
Complexes of the H 5 O 2 + and H 3 O + cations with polyethers in water saturated dichloroethane solutions. A combined IR spectroscopic and quantum mechanics study.
J. Chem. Soc., Perkin Trans. 2, 2002, 887-893.

V. Torgov, S. Erenburg, N. Bausk, E. Stoyanov, V. Kalchenko, A. Varnek , G. Wipff
The structure of new heterometallic Ru / M (M = Cu, Ni, Co, Zn) complexes investigated by combined spectroscopic and modelling studies.
J. Mol. Struct., 2002, 611 , 131-138.

Hamdane M, Smet C, Sambo AV, Leroy A, Wieruszeski JM, Delobel P, Maurage CA, Ghestem A, Wintjens R, Begard S, Sergeant N, Delacourte A, Horvath D, Landrieu I, Lippens G, Buee L
Pin1 - A therapeutic target in Alzheimer neurodegeneration
JOURNAL OF MOLECULAR NEUROSCIENCE, 19(3), 275-287, 2002

Penzotti JE, Mao B, Horvath D, Migeon J, Krejsa C, Porubek D
Exploring the relationships between chemical structure, in vitro profiles, and in vivo behavior.
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 223, U349-U349

Elezgaray J, Marcou G, Sanejouand YH
Exploring the natural conformational changes of the C-terminal domain of calmodulin
PHYSICAL REVIEW E, 66(3), 2002

Poulain B, Horvath D, Bonnet B, Eckhoff C, Chapelain B, Bodinier MC, Deprez B
From hit to lead. Combining two complementary methods for focused library design. Application to mu opiate ligands Record contains structures
JOURNAL OF MEDICINAL CHEMISTRY, 44(21), 3378-3390, 2001

Poulain R, Horvath D, Bonnet B, Eckhoff C, Chapelain B, Bodinier MC, Deprez B
From hit to lead. Analyzing structure-profile relationships Record contains structures
JOURNAL OF MEDICINAL CHEMISTRY, 44(21), 3391-3401, 2001

Horvath D
Recursive Partitioning analysis of mu-opiate receptor high throughput screening results
SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 12(1-2), 181-212, 2001

Elezgaray J, Marcou G, Sanejouand YH
Coupling overall rotations with modal dynamics Context Sensitive Links
THEORETICAL CHEMISTRY ACCOUNTS, 106(1-2), 62-68, 2001

A.V. Solovyov, L.I. Atamas, O.V. Klimchuk, V.L. Rudzevich and V.I. Kalchenko, A. Varnek and G. Wipff.
Ionophores Based on of Calix[4]arenes Phosphorylated at the Upper Rim.
EURADWASTE 1999 "Radioactive Waste Management. Strategies and Issues ", p. 523-526, 2000, Luxembourg. European Communities.

S. Meyer, R. Louis, B. Metz, Y. Agnus, A. Varnek , M. Gross
Unprecedented Role of Water in Self-Assembly of Potential Molecular Tweezers
New J. Chem., 2000, 24, 371-376.

V. P. Solov’ev, A. Varnek , G. Wipff
Modelling of Ion Complexation and Extraction of Organic Molecules Using Substructural Molecular Fragments
Chem. Inf. Comp. Sci., 2000, 40, 847-858

Horvath D, Jeandenans C
Molecular similarity and virtual screening. In silico methods to retrieve active analogs in the context of discovering therapeutic compounds
ACTUALITE CHIMIQUE, 9, 64-67, 2000

53. A. Varnek, G. Wipff, A. Bilyk, J. Harrowfield
Molecular Dynamics and Free Energy Perturbation Studies of Ca2+/Sr2+ Complexation Selectivities of the Macrocyclic Ionophores DOTA and TETA in Water.
J. Chem. Soc., Dalton Trans, 1999, 23, 4155.

Frank Hoonakker, Alexandre Varnek and Alain Wagner
A computer based method for calculate similarity between two reactions based on the concept of Condensed Graph of Reactions.
US 11/779 255, PCT/IB2008/052851 from 17.07.2008

A.Yu.Tsivadze, A.A.Varnek, V.E.Khutorsky
Coordination Compounds of Metals with Crown-Ligands (Russ), Nauka Publ. House, Moscow, 1991, 396 pp.

"Chemoinformatics Approaches to Virtual Screening", A. Varnek and A. Tropsha, Eds., RSC Publishing, 2008

Alexandre Varnek and Vitaly Solov’ev
Quantitative Structure-Property Relationships in Solvent Extraction and Complexation of Metals.
In “Ion Exchange and Solvent Extraction”, Vol. 19, B. A. Moyer and A. K. Sengupta, Eds., Taylor and Francis : Philadelphia, 2009.

Igor Baskin and Alexandre Varnek
Fragment Descriptors in SAR/QSAR/QSPR Studies, Molecular Similarity Analysis and in Virtual Screening.
In “Chemoinformatics Approaches to Virtual Screening”, A. Varnek and A. Tropsha, Eds., RSC Publishing, 2008

Alexandre Varnek
Fragment Descriptors in Structure-Property Modeling and Virtual Screening.
In : "Chemoinformatics and Computational Chemical Biology", J. Bajorath, Ed., Springer, 2010