Publications


2017

P.Sidorov, B.Viira, E.Davioud-Charvet, U.Maran, G. Marcou, D. Horvath and A. Varnek
QSAR modeling and chemical space of antimalarial compounds
J. Comput. Aided Mol. Des., 2017, 31(5), 441-445, DOI: 10.1007/s10822-017-0019-4

D. Horvath, I. Baskin, G. Marcou and A. Varnek
Generative Topographic Mapping of conformational space
Mol. Informatics, accepted 30.03.2017

S. Kayastha, D. Horvath, E. Gilberg, M. Gütschow, J. Bajorath and A. Varnek
Priviledged structural motif detection and analysis using Generative Topographic Maps
J. Chem. Inf. Model., 2017, 56(5), 1218-1232

I.I. Baskin, V.P. Solov'ev, A.A. Bagaturyans and A. Varnek
Predictive cartography of metal binders using Generative Topographic Mapping
J. Comput. Aided Mol. Des., 2017, accepted

K. Klimenko, S. Lyakhov, M. Shibinskaya, A. Karpenko, G. Marcou, D. Horvath, M. Zenkova, E. Goncharova, R. Amirkhanov, S. Andronati, P. Polishchuck, V. Kuz'min and A. Varnek
Virtual screening, synthesis and biological evaluation of DNA intercalating antiviral agents
Bioorgan. Med. Chem. lett., 2017, accepted

G. Marcou, D. Horvath and A. Varnek
Neighboring structure visualization on a grid-based layout
Mol. Informatics, 2017, accepted

P. Polishchuck, T. Madzhidov, T. Gimadiev, A. Bodrov, R. Nugmanov and A. Varnek
Structure-reactivity modeling using mixture-based representation of chemical reactions
J. Comput. Aided Mol. Des., 2017, accepted

2016

A.I. Lin, T.I. Madzhidov, O. Klimchuk, R.I. Nugmanov, I.S. Antipin and A. Varnek
Assessment of protective group reactivity from big data analysis
J. Chem. Inf. Model., 2016, DOI: 10.1021/acs.jcim.6b00319

D. Horvath, G. Marcou, A. Varnek, S. Kayastha, A. de la Vega de Leon and J. 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., 2016, 56(9), 1631-1640

T.R. Gimadiev, T.I. Madzhidov, G. Marcou and A. Varnek
Generative Topographic Mapping approaches to modeling and chemical space visualization of Human Intestinal Transporters
BioNanoScience, 2016, DOI: 10.1007/s12668-016-0246-5

P. Polishchuk, O. Tinkov, T. Khristova, L. Ognichenko, A. Kosinskaya, A. Varnek and V. Kuz'min
Structural and physico-chemical interpretation (SPCI) of QSAR models and its comparison with MMP analysis
J. Chem. Inf. Model., 2016, 56, 1455-1469

K. Klimenko, G. Marcou, D. Horvath and A. Varnek
Chemical space mapping and structure-activity analysis of the ChEMBL antiviral compound set.
J. Chem. Inf. Model., 2016, 56, 1438-1454

M. Glavatskikh, T. Madzhidov, V. Solov’ev, G. Marcou, D. Horvath, J. Graton, J.-Y. Le Questel and A. Varnek
Predictive models for halogen-bond basicity of binding sites of polyfunctional molecules
Mol. Informatics, 2016, 35(2), 70-80

M. Glavatskikh, T. Madzhidov, V. Solov'ev, G. Marcou, D. Horvath and A. Varnek
Predictive Models for the Free Energy of Hydrogen Bonded Complexes with Single and Cooperative Hydrogen Bonds
Mol. Informatics, 2016, DOI: 10.1002/minf.201600070

B. Viira, T. Gendron, D.A. Lanfranchi, S. Cojean, D. Horvath, G. Marcou, A. Varnek, L. Maes, U. Maran, P. Loiseau and E. Davioud-Charvet
In Silico Mining for Antimalarial Structure-Activity Knowledge and Discovery of Novel Antimalarial Curcuminoids
Molecules, 2016, 21(7), 853, DOI: 10.3390/molecules21070853

K. Mansouri, A. Abdelaziz, A. Rybacka, A. Roncaglioni, A. Tropsha, A. Varnek, A. Zakharov, A. Worth, A.M. Richard, C.M. Grulke, D. Trisciuzzi, D. Fourches, D. Horvath, E. Benfenati, E. Muratov, E. Bay Wedebye, F. Grisoni, G.F. Mangiatordi, G.M. Incisivo, H. Hong, H.W. Ng, I.V. Tetko, I. Balabin, J. Kancherla, J. Shen, J. Burton, M. Nicklaus, M. Cassotti, N.G. Nikolov, O. Nicolotti, P.L. Andersson, Q. Zang, R. Politi, R.D. Beger, R. Todeschini, R. Huang, S. Farag, S.A. Rosenberg, S. Slavov, X. Hu and R.S. Judson
CERAPP : Collaborative Estrogen Receptor Activity Prediction Project
Environ. Health Perspect., 2016, accepted, DOI: 10.1289/ehp.1510267

P. Sidorov, I. Desta, M. Chessé, D. Horvath, G. Marcou, A. Varnek, E. Davioud-Charvet and M. Elhabiri
Redox Polypharmacology as an Emerging Strategy to Combat Malarial Parasites
ChemMedChem, 2016, accepted, DOI: 10.1002/cmdc.201600009

G. Marcou, D. Horvath and A. Varnek
Kernel Target Alignment parameter - a new modelability measure for regression tasks
J. Chem. Inf. Model., 2016, 56(1), 6-11

2015

G. Marcou, J. Aires de Sousa, D. Latino, A. Deluca, D. Horvath, V. Rietsch, and A. Varnek
Towards an expert system for predicting reaction conditions: the Michael reaction case.
JCIM, 2015, 55(2), 239-250. DOI: 10.1021/ci500698a

C. Muller, D. Pekthong, C. Desbans, E. Alexandre, G. Marcou, L. Richert and A. Varnek
Prediction of DILI using molecular and biological descriptors
Comb. Chem. High. T. Scr., 2015, 18(3). DOI:10.2174/1386207318666150305144650

H. Gaspar, I.I. Baskin, G. Marcou, D. Horvath and A. Varnek
Chemical Data Visualization and Analysis with Incremental GTM: Big Data Challenge
J. Chem. Inf. Model., 2015, 55(1), 84–94

H.A. Gaspar, I.I. Baskin, G. Marcou, D. Horvath and A. Varnek
GTM-based QSAR models and their applicability domains
Mol. Informatics, 2015, 34 (6-7), 348-356  

T. Khristova, P. Polishchuk, A. Varnek and V. Kuzmin
Computer-aided design of new antagonists of thromboxane receptors acting as anti-aggregation agents
Dopovidi NASU. (ukr), 2014, N°9, 103-108

L. Hoffer, C. Chira, G. Marcou, A. Varnek and D. Horvath
S4MPLE – Sampler For Multiple Protein-Ligand Entities. I. Methodology & Rigid-Site Docking Benchmarking
Molecules, 2015, 20, 8997-9028, DOI:10.3390/molecules20058997

C. Muller, A.G. Maldonado, A. Varnek and B. Creton
Prediction of optimal salinities for surfactant formulations using QSPR approaches.
Energy and Fuels, 2015, 29 (7), 4281–4288.

M. Elhabiri, P. Sidorov, E. Cesar-Rodo, G. Marcou, D.A. Lanfranchi, E. Davioud-Charvet, D. Horvath and A. Varnek
Electrochemical Properties of Substituted 2-Methyl-1,4-Naphthoquinones: Redox Behavior Predictions
Chem. Eur. J., 2015, 21(8), 3415-3424

P.G. Polishchuk, G.V. Samoylenko, T.M. Khristova, O.L. Krysko, T.A. Kabanova, V.M. Kabanov, A.Y. Kornylov, O. Klimchuk, T. Langer, S.A. Andronati,V.E. Kuz’min, A.A. Krysko and A. Varnek
Virtual screening, design and synthesis of antagonists of αIIbβ3 as antiplatelet agents
J. Med. Chem., 2015, 58 (19), pp 7681–7694, DOI 10.1021/acs.jmedchem.5b00865

H.A. Gaspar , I.I. Baskin, G. Marcou, D. Horvath and A. Varnek
Stargate GTM: bridging descriptor and activity spaces.
J. Chem. Inf. Model., 2015, 55 (11), 2403–2410, DOI:10.1021/acs.jcim.5b00398

T. Madzhidov, A. Bodrov, T. Gimadiev, R. Nugmanov, I. Antipin and A. Varnek
Obtaining structure-reactivity relationships for bimolecular elimination reactions with Condensed Reaction Graph approach
J. Struct. Chem. (Russ), 2015, 56 (7), 1227 – 1234

C. Muller, D. Pekthong, E. Alexandre, G. Marcou, D. Horvath, L. Richert and A. Varnek
Prediction of Drug Induced Liver Injury Using Molecular and Biological Descriptors
Comb. Chem. High. T. Scr., 2015, 18(3), 315-322

P. Sidorov, H. A. Gaspar, Helena; A. Varnek, G. Marcou and D. Horvath
Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds
J Comput Aided Mol Des. 2015, 29(12):1087-1108

T. Madzhidov, R. Nugmanov, T. Gimadiev, A. Lin, I. Antipin and A. Varnek
Consensus approach to atom-to-atom mapping in chemical reactions
Butlerov Communications 2015; 44(12), 170-176

Тимур Маджидов, Рамиль, Нугманов, Тимур Гимадиев, Аркадий Лин, Игорь Антипин Александр Варнек
Консенсусный подход к созданию атом-атомного отображения в химических реакциях,
Butlerov Comminications, 2015, accepted

2014

F. Ruggiu, P. Gizzi, J.-L. Galzi, M. Hibert, J. Haiech, I. Baskin, D. Horvath, G. Marcou and A. Varnek
Quantitative Structure-Property Relationship Modeling: A Valuable Support in High-Throughput Screening Quality Control
Anal. Chem., 2014, 86(5), 2510-2520

E. Le Louarn, A. Barbaud, P. Trechot, G. Marcou and J.-P. Lepoittevin
The use of three-dimensional similarity in assessing the risk of cross-reactivity between carbamazepine and psychotropic drugs
Eur. J. Clin. Pharmacol., 2014, 70(4), 495-498

J.-B. Brown, Y. Okuno, G. Marcou, A. Varnek and D. Horvath
Computational chemogenomics: Is it more than inductive transfer?
JCAMD, 2014, 28(6), 597-618

F. Ruggiu, V. Solov’ev, G. Marcou, D. Horvath, J. Graton, J.-Y. Le Questel and A. Varnek
Individual Hydrogen-Bond Strength QSPR Modelling with ISIDA Local Descriptors: a Step Towards Polyfunctional Molecules,
Mol. Inf., 2014, 33(6-7), 477-487

V. Chupakhin, G. Marcou, H. Gaspar and A. Varnek
Simple Ligand-Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison
Comput. Struct. Biotechnol. J., 2014, 10, 33-37

D. Horvath, M. Lisurek, B. Rupp, R. Kühne, E. Specker, J. von Kries, D. Rognan, C.D. Andersson, F. Almqvist, M. Elofsson, P.-A. Enqvist, A.-L. Gustavsson, N. Remez, J. Mestres, G. Marcou, A. Varnek, M. Hibert, J. Quintana and R. Frank
Design of a General-Purpose European Compound Screening Library for EU-OPENSCREEN,
Chem. Med. Chem., 2014, 9(10), 2309-2326

A. Cherkasov, E. Muratov, D. Fourches, A. Varnek, I. Baskin, M. Cronin, J. Dearden, P. Gramatica, Y. Martin, R. Todeschini, V. Consonni, V. Kuz'min, R. Cramer, R. Benigni, C Yang, A. Richard, L. Terfloth, J. Gasteiger, and A. Tropsha
QSAR Modeling: Where have you been? Where are you going to?
J. Med. Chem., 2014, 57 (12), 4977-5010 

T.I. Madzhidov, P.G. Polishchuk, R.I. Nugmanov, A.V. Bodrov, A.I. Lin, I.I. Baskin, I.S. Antipin and A.A. Varnek
Structure-reactivity relationships in terms of the condensed graphs of reactions
Russ. J. Org. Chem., 2014, 50 (4), 459-463

V. Solov’ev, A. Varnek and A. Tsivadze
QSPR Ensemble Modelling of the 1:1 and 1:2 Complexation of Co2+, Ni2+, and Cu2+ with Organic Ligands. Relationships between Stability Constants
Computer Aided Mol. Design, 2014, 28,549–564

D. Rognan and A. Varnek
A Summer School for Structuring the Chemoinformatics Community
Mol. Informatics, 2014, 33 (6-7), 390

R.I. Nugmanov, T.I. Madzhidov, G.R. Haliullina, I.I. Baskin, I.S. Antipin, A. Varnek
Development of "structure-reactivity" models for nucleophilic substitution reactions with participation of azides
J. Struct. Chem. (Russ), 2014, 55 (6), 1080 – 1087

D. Horvath, J.B. Brown, G. Marcou and A. Varnek
An Evolutionary Optimizer of libsvm Models
Challenges, 2014, 5(2), 450-472

G.V. Sitnikov, N.I. Zhokhova, Y.A. Ustynyuk, A. Varnek and I.I. Baskin
Continuous Indicator Fields – A Novel Universal Type of Molecular Fields
JCAMD, accepted, november 2014, DOI 10.1007/s10822-014-9818-z

Т.М. Христова, П.Г. Полищук, А.А. Варнек, В.Е. Кузьмин
Целенаправленный поиск новых антиагрегационных средств в ряду антагонистов тромбоксановых рецепторов
Dopovidi NASU. (ukr), 2014, N°9

2013

I. Oprisiu, G. Marcou, D. Horvath, B. Brunel, F. Rivollet and A. Varnek
Publicly available models to predict normal boiling point of organic compounds
Themochim. Acta, 2013, 553, 60-67

V. Chupakhin, G. Marcou, I. Baskin, A. Varnek and D. Rognan
Predicting Ligand Binding Modes from Neural Networks Trained on Protein-Ligand Interaction Fingerprints
JCIM, 2013, 53(4), 763-772

D. Horvath, G. Marcou and A. Varnek
Do Not Hesitate to Use Tversky-and Other Hints for Successful Active Analogue Searches with Feature Count De-
scriptors
JCIM, 2013, 53(7), 1543-1562

H. Gaspar, G. Marcou, D. Horvath, A. Arault, S. Lozano, P. Vayer and A. Varnek
Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the
Biopharmaceutics Drug Disposition Classification System (BDDCS)
JCIM, 2013, 53(12), 3318-3325

A.A. Krysko, G.V. Samoylenko, P.G. Polishchuk, M.S. Fonari, V.C. Kravtsov, S.A. Andronati, T.A. Kabanova, J. Lipkowski, T.M. Khristova, V.E. Kuz'min, V.M. Kabanov, O.L. Krysko, and A.A. Varnek
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 alpha(IIb)beta(3)
Bioorgan. Med. Chem., 2013, 21(15), 4646-4661

P.N.W. Baxter, J.-P. Gisselbrecht, L. Brelot, A. Varnek and L. Allouche
Synthesis of a Strained Acetylenic Macrocycle Incorporating a para-Oligo[2]cruciform Bridge Bent over Nanoscopic Dimensions: Structural, Electronic, Spectroscopic and Ion-Sensing Properties.
Chem. Eur. J., 2013, 19(37), 12336-12349

P.G. Polishchuk, T.I. Madzhidov and A. Varnek
Estimation of the size of drug-like chemical space based on GDB-17 data
J. Comput. Aided Mol. Des., 2013, 27, 675–679

D. Beltrami, A. Chagnes, M. Haddad, A. Varnek, H. Mokhtari, B. Courtaud and G. Cote
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
Hydrometallurgy, 2013, 140, 28–33

V.P. Solov’ev, N. Kireeva, A.Y. Tsivadze and A. Varnek,
QSPR Consensus Models for Alkaline-Earth Metal Complexation
J. Incl. Phenom. Macro., 2013, 76(1), 159-171

2012

P.N.W. Baxter, A. Al-Ouahabi, J.-P. Gisselbrecht, L. Brelot, A. De Cian and A. 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

F. Bonachera, G. Marcou, N. Kireeva, A. Varnek and D. Horvath
Using Self-Organizing Maps to Accelerate Similarity Search
Bioorg. Med. Chem., 2012, 20(18), 5396-5409

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

I. Oprisiu, E. Varlamova, E. Muratov, A. Artemenko, G. Marcou, P. Polishchuk, V. Kuz’min and 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 and A. Varnek
Interpretability of SAR/QSAR models of any complexity by atomic contributions
Mol. Inf., 2012, 31(9), 639-642, 2012

A. de Luca, D. Horvath, G. Marcou, V.P. Solov’ev and A. Varnek
Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions approach.
J. Chem. Inf. Model. 2012, 52(9), 2325-2338

V. Solov’ev V, I. Sukhno, V. Buzko, A. Polushin, G. Marcou, A.Tsivadze and A. Varnek
Stability constants of complexes of Zn2+, Cd2+, and Hg2+ with organic ligands: QSPR consensus modeling and design of new metal binders
J. Incl. Phenom. Macro., 2012, 72(3-4), 309-321

V. Solov’ev, G. Marcou, A. Tsivadze and A. Varnek
Complexation of Mn2+, Fe2+, Y3+, La3+, Pb2+, and UO22+ with Organic Ligands: QSPR Ensemble Modeling of Stability Constants,
Ind. & Eng. Chem. Res., 2012, 51(41), 13482-13489

C. Muller, G. Marcou, D. Horvath, J. Aires-de-Sousa and A. Varnek
Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms
JCIM, 2012, 52(12), 3116-3122

E. Kondratovich, I.I. Baskin and A. Varnek
Transductive Support Vector Machines: promising approach to model small, unbalanced and diverse datasets
Mol. Inf., 2012, 32 (3), 261-266

V. Solov’ev, A. Tsivadze and A. Varnek
New Approach for Accurate QSPR Modeling of Metal Complexation: Application to Stability Constants of Lanthanide Ions Ln3+, Ag+, Zn2+, Cd2+ and Hg2+ with Organic Ligands in Water
Macroheterocycles (Russ), 2012, 5 (4-5), 404-410

2011

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

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

C. Koch, G. Schneider, G. Marcou, A. Varnek and D. Horvath
Local Neighborhood Behavior : Study of a Combinatorial Library Context
J. Comput. Aid. Mol. Des., 2011, 25:237–252

I. Sushko, A.K. Pandey, S. Novotarskyi, R. Körner, M. Rupp, W. Teetz, S. Brandmaier, A. Abdelaziz, V.V. Prokopenko, V.Y. Tanchuk, R. Todeschini, A. Varnek, G. Marcou, P. Ertl, V. Potemkin, M. Grishina, J. Gasteiger, I.I. Baskin, V.A. Palyulin, E.V. Radchenko, W.J. Welsh, V. Kholodovych, D. Chekmarev, A. Cherkasov, J. Aires-de-Sousa, Q.-Y. Zhang, A. Bender, F. Nigsch, L. Patiny and I.V. Tetko
Online Chemical Modeling Environment (OCHEM) : Web Platform for Data Storage, Model Development and Publishing of Chemical Information
J. Comput. Aid. Mol. Des., 2011, 25 (6), 533-54.

F. Hoonakker, N. Lachiche, A. Varnek and A. Wagner
Condensed Graph of Reaction : considering a chemical reaction as one single pseudo molecule
Int. J. Artif. Intel. T., 2011, 20, (2), 253-270

A.A. Krysko, G.V. Samoylenko, P.G. Polishchuk, S.A. Andronati, T.A. Kabanova, T.M. Khristova, V.E. Kuz’min, V.M. Kabanov, O.L. Krysko, A.A. Varnek and R.Yu. Grygorash
RGD mimetics containing phthalimidine fragment, novel ligands of fibrinogen receptor.
Bioorg. Med. Chem. Lett., 2011, 21, 5971–5974

V.P. Solov’ev, I. Oprisiu, G. Marcou and A. Varnek
QSPR Modeling of Normal Boiling Point Temperature and Composition of Binary Azeotropes
Ind. Eng. Chem. Res., 2011, 50 (24), 14162–14167

G. Marcou, I. Billard, A. Ouadi and A. Varnek
In silico design of new ionic liquids (ILs) based on QSPR models of ILs viscosity
J. Phys. Chem. B, 2011, 115 (1), 93–98

2010

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

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

F. Hoonakker, N. Lachiche, A. Varnek and A. 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).

I. Sushko, S. Novotarskyi, R. Korner, A.K. Pandey, J. Li, P. Gramatica, K. Hansen, T. Schroeter, K.-R. Muller, L. Xi, H. Liu, X. Yao, T.s Oberg, A. Cherkasov, F. Hormozdiari, P. Dao, C. Sahinalp, R. Todeschini, D. Fourches, E. Muratov, A. Tropsha, I. Baskin, D. Horvath, G. Marcou, C. Muller, A. Varnek, V.V. Prokopenko, and I.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

F. Ruggiu, G. Marcou, A. Varnek and D. Horvath
ISIDA Property-labeled fragment descriptors
Mol. Informatics, 2010, 29, 855 – 868

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

2009

D. Horvath, G. Marcou and A. Varnek
Predicting the Predictability : A Unified Approach to the Applicability Domain Problem of QSAR Models
J. Chem. Inf. Model., 2009, 49(7), 1762-1776

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

A. Varnek, C. Gaudin, G. Marcou, I. Baskin, A.K. Pandey and I.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., 2009, 49(1), 133-144

2008

H. Zhu, D. Fourches, A. Varnek, E. Papa, P. Gramatica, I.V. Tetko, T. Öberg, A. Cherkasov and A. Tropsha
Combinational QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis
J. Chem. Inf. Mod., 2008, 48, 766-784

I.V. Tetko, I. Sushko, A.K. Pandey, H. Zhu, A. Tropsha, E. Papa, T. Öberg, R. Todeschini, D. Fourches and A. Varnek
Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: Focusing on applicability domain and overfitting by variable selection
J. Chem. Inf. Mod., 2008, 48, 1733-1746

A. Varnek, D. Fourches, D. Horvath, O. Klimchuk, C. Gaudin, P. Vayer, V. Solov’ev, F. Hoonakker, I.V. Tetko and G. Marcou
ISIDA - Platform for virtual screening based on fragment and pharmacophoric descriptors
Curr. Comput. Aid. Drug., 2008, 4(3), 191-198

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

C. Barillari, G. Marcou and D. Rognan
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
J. Chem. Inf. Model., 2008, 48(7), 1396-1410

A.A. Tantar, S. Conilleau, B. Parent, N. Melab, L. Brillet, S. Roy, E.G. Talbi and D. Horvath
Docking and biomolecular simulations on computer grids : Status and trends
Curr. Comput. Aid. Drug., 2008, 4(3), 235-249

F. Bonachera and D. Horvath
Fuzzy tricentric pharmacophore fingerprints. 2. application of topological fuzzy pharmacophore triplets in quantitative structure-activity relationships
J. Chem. Inf. Model., 2008, 48(2), 409-425

2007

G.Kostin, A. Borodin, V. Emel`yanov, D. Naumov, A. Virovets, M.-M. Rohmer and A. Varnek
Synthesis and structure of heterometallic compounds of [RuNO(NO2)4OH]2- with triphenilphosphineoxide complexes of Co(II), Ni (II) and Zn(II).
J. Mol. Structure, 2007, 837, 63-71

A. Varnek, N. Kireeva, I.V. Tetko, I.I. Baskin and V.P. Solov'ev
Exhaustive QSPR studies of large diverse set of ionic liquids: how accurately can we predict the melting point?
J. Chem. Inf. Mod., 2007, 47, 1111-1122

A. Varnek, D. Fourches, V. Solov'ev, O. Klimchuk, A. Ouadi and I. Billard
Successful « In Silico » Design of New Efficient Uranyl Binders
J. Solv. Extr. Ion Exch., 2007, 25, N°4, 433-462

D. Horvath, F. Bonachera , V. Solov'ev , C. Gaudin and A. Varnek
Stochastic versus Stepwise Strategies for Quantitative Structure-Activity Relationship Generation - How much effort may the mining for successful QSAR models take?
J. Chem. Inf. Mod., 2007,47 (3), 927-939

A. Varnek, D. Fourches, N. Sieffert, V.P. Solov’ev, C. Hill and M. Lecomte
QSPR modelling of the AmIII/EuIII separation factor : how far can we predict ?
J. Solv. Extr. Ion. Exch., 2007, 25, 1-26

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

G. Marcou and D. Rognan
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
J. Chem. Inf. Model., 2007, 47(1), 195-207

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

B. Parent, A. Kokosy and D. Horvath
Optimized evolutionary strategies in conformational sampling
Soft Comput., 2007, 11(1), 63-79

2006

A.R. Katritzky, M. Kuanar, S. Slavov, D.A. Dobchev, D.C. Fara, M. Karelson, W.E. Acree Jr., V.P. Solov’ev and A. Varnek
Correlation of Blood : Brain Barrier Permeation Using Structural Descriptors.
Bioorgan. Med. Chem., 2006, 14, 4888-4917

S. Mari, F.J. Canada, J. Jimenez-Barbero, A. Bernardi, G. Marcou, I. Motto, I. Velter, F. Nicotra and B. La Ferla
Synthesis and conformational analysis of galactose-derived bicyclic scaffolds Record contains structures
Eur. J. Org. Chem., 2006, 13, 2925-2933

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

I.V. Tetko, V.P. Solov’ev, A.V. Antonov, X. Yao, J.-P. Doucet, B. Fan, F. Hoonakker, D. Fourches, P. Jost, N. Lachiche and A. 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 and A. A. Varnek
Structure – property modelling of complexation of strontium cation by organic ligands
J. Struct. Chem., 2006, 47, 311-325

F. Bonachera, B. Parent, F. Barbosa, N. Froloff, D. Horvath D
Fuzzy tricentric pharmacophore fingerprints. 1. Topological fuzzy pharmacophore triplets and adapted molecular similarity scoring schemes
J. Chem. Inf. Model,2006, 46(6), 2457-2477

2005

A. Varnek and V.P. Solov’ev
“In silico” design of potential anti-HIV actives using fragment descriptors
Comb. Chem. High. T. Scr., 2005, 8, 403-416.

V. Torgov, G. Kostin, T. Korda, E. Stoyanov, V. Kalchenko, A. Drapailo, O. Kasyan, G. Wipff and 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 and A. Varnek
QSAR Modeling of Blood:Air and Tissue:Air Partition Coefficients Using Theoretical Descriptors
Bio-orga. Med. Chem., 2005, 13(23), 6450-6463.

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

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

R. Gozalbes, C. Rolland, E. Nicolai, M.F. Paugam, L. Coussy, D. Horvath, F. Barbosa, B. Mao, F. Revah and N. Froloff
QSAR strategy and experimental validation for the development of a GPCR focused library
QSAR Comb. Sci., 2005, 24(4), 508-516

2004

A. Varnek, D. Fourches and V. P. Solov’ev
In silico design of new compounds using fragment descriptors.
In QSAR and Molecular Modelling in Rational Drug Design of Bioactive Molecules, E. Aki-Sener and I. Yalcin, Eds., CADD&D, Ankara, Turkey, 2004, 342-345

V. P. Solov’ev and 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 and 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 and G. Wipff
New wide rim phosphomethylated calix[4]arenes in extraction of actinides and lanthanides
J. Inclusion Phenom. Macrocyclic Chem., 2004, 49, 47-56

A.R. Katritzky, D.C. Fara, H. Yang, M. Karelson, T. Suzuki, V.P. Solov’ev and A. Varnek
QSPR Modeling of b - Cyclodextrin Complexation Free Energies
J. Chem. Inf. Comp. Sci., 2004, 44, 529-541

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

F. Barbosa and D. Horvath
Molecular similarity and property similarity
Curr. Top. Med. Chem., 2004, 4(6), 589-600

S. Mari, H. Posteri, G. Marcou, D. Potenza, F. Micheli, F.J. Cañada, J.J. Jiménez-Barbero and A. Bernardi
Synthesis, conformational studies and mannosidase stability of a mimic of 1,2-mannobioside.
Eur. J. Org. Chem., 2004, 5119-5125

2003

D. Fourches, V. Solov’ev and A. Varnek
“In silico” design of new potential metal binders
Congrès “Chimiomètrie 2003, 3 4 décembre 2003, Paris, France, Abstracts, p. 129 – 132, Groupe Français de Chimiomètrie, 2003.

V.P. Solov’ev and 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

J.C. Migeon, S.L. Rogalski, C.M. Krejsa, D. Horvath, B. Mao, F. Barbosa, S.E. Merrick, M. Mersberg and F. Lakehal
Using large in vitro ADME data sets to predict in vivo properties
Drug Metab. Rev., 2003, 35, 168-168

C.M. Krejsa, D. Horvath, S.L. Rogalski, J.E. Penzotti, B. Mao, F. Barbosa, J.C. Migeon JC
Predicting ADME properties and side effects : The BioPrint approach
Curr. Opin. Drug Di. De., 2003, 6(4), 470-480

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

D. Horvath and C. Jeandenans
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
J. Chem. Inf. Comp. Sci., 2003, 43(2), 680-690

D. Horvath and C. Jeandenans
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
J. Chem. Inf. Comp. Sci., 2003, 43(2), 691-698

2002

L. Atamas, O. Klimchuk, V. Rudzevich, V. Kalchenko, V. Pirozhenko, I. Smirnov, V. Babain, T. Efremova, A. Varnek, G. Wipff, F. Arnaud-Neu, M. Roch, M. Saadioui and V. Böhmer,
New organophosphorus calix[4]arene ionophores for trivalent lanthanide and actinide cations.
J. Supramol. Chem., 2002, 2, 421-427.

Yu.Rudzevich, A. Drapaylo, V. Rudzevich, V. Miroshnichenko, V. Kalchenko, I. Smirnov, V. Babain, A. Varnek and 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 and 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 and 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 and 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 and E. Stoyanov
Complexes of the H5O2+ and H3O+ 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 and, 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.

M. Hamdane, C. Smet, A.V. Sambo, A. Leroy, J.-M. Wieruszeski, P. Delobel, C.A. Maurage, A. Ghestem, R. Wintjens, S. Begard, N. Sergeant, A. Delacourte, D. Horvath, I. Landrieu, G. Lippens and L. Buee
Pin1 - A therapeutic target in Alzheimer neurodegeneration
J. Mol. Neurosci., 2002, 19(3), 275-287

J.E. Penzotti, B. Mao, D. Horvath, J. Migeon, C. Krejsa, D. Porubek
Exploring the relationships between chemical structure, in vitro profiles, and in vivo behavior.
Abstr. Pap. Am. Chem. S., 2002, 223, U349-U349

J. Elezgaray, G. Marcou, Y.H. Sanejouand
Exploring the natural conformational changes of the C-terminal domain of calmodulin
Phys. Rev. E., 2002, 66(3)

2001

A. Varnek , G. Wipff and V.P. Solov’ev
Towards an information system on solvent extraction
J. Solvent Extract. Ion. Exch., 2001, 19(5), 791 - 837

R. Poulain, D. Horvath, B. Bonnet, C. Eckhoff, B. Chapelain, M.C. Bodinier and B. Deprez
From hit to lead. Combining two complementary methods for focused library design. Application to mu opiate ligands Record contains structures
J. Med. Chem., 2001, 44(21), 3378-3390

R. Poulain, D. Horvath, B. Bonnet, C. Eckhoff, B. Chapelain, M.C. Bodinier and B. Deprez
From hit to lead. Analyzing structure-profile relationships Record contains structures
J. Med. Chem., 2001, 44(21), 3391-3401

D. Horvath
Recursive Partitioning analysis of mu-opiate receptor high throughput screening results
SAR QSAR Environ. Res., 2001, 12(1-2), 181-212

J. Elezgaray, G. Marcou and Y.H. Sanejouand
Coupling overall rotations with modal dynamics Context Sensitive Links
Theor. Chem. Acc., 2001, 106(1-2), 62-68

2000

A. Varnek, B. Dietrich, G. Wipff, J.-M. Lehn and E.V. Boldyreva
SUPRAMOLECULAR CHEMISTRY: computer assisted instruction in undergraduate and graduate chemistry courses
J. Chem. Educat., 2000, 77, 222-226

E. Stoyanov, I. Smirnov, A. Varnek and G. Wipff
Microscopic Insights into Synergistic Effects : Sr(II) Extraction by a Mixture of Chlorinated Cobalt Dicarbollide and Polyethers.
EURADWASTE 1999 "Radioactive Waste Management. Strategies and Issues ", 2000, p. 519-522, Luxembourg. European Communities.

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 ", 2000, p. 523-526, Luxembourg. European Communities.

S. Meyer, R. Louis, B. Metz, Y. Agnus, A. Varnek and 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 and G. Wipff
Modelling of Ion Complexation and Extraction of Organic Molecules Using Substructural Molecular Fragments
Chem. Inf. Comp. Sci., 2000, 40, 847-858

A. Varnek, T. Volkova, O.M. Petrukhin and G. Wipff
Switching of Ba2+/Ca2+ into Ba2+/Ca2+ Potentiometric Selectivities of Podlands with Phosphoryl-Containing Terminal Groups. A Molecular Modelling Study.
J. Incl. Phenom. 2000, 37, 407-421

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

1999

A. Varnek and G. Wipff
Molecular Modelling in Solvent Extraction: Ionophores in Pure Solutions and at the Liquid/Liquid Interface
J. Solvent Extract. Ion. Exch., 1999, 17(6), 1493-1505

A.Y. Nazarenko, J.D. Lamb, V.E. Baulin, T. Volkova, A. Varnek and G. Wipff
Solvent extraction of Metal Ion Picrates with Phosphine Oxide Podands
J. Solvent Extract. Ion. Exch., 1999, 17, 495-523

A. Varnek, G. Wipff, A. Bilyk and 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.

J.R.C. Garry, M.C. Towner, A.J. Ball, J.C. Zarnecki and G Marcou
The effect of ambient pressure and impactor geometry on low speed penetration of unconsolidated materials,
Adv. Space. Res., 1999, 23 (7), 1229-1234

Patents

F. Hoonakker, A. Varnek and A. 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

Monograph

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

Edited Books

"Tutorials in Chemoinformatics", A. Varnek (Ed), WILEY, 2017

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


Text Books

I.I. Baskin, T.I. Madzhidov and A.A. Varnek
Introduction into Chemoinformatics. Machine-Learning Methods (Russ)
University of Kazan, Kazan, 2016, 302 pp., ISBN 978-5-00019-442-3

I.I. Baskin, T.I. Madzhidov and A.A. Varnek
Introduction into Chemoinformatics. “Structure-Property” modeling, (Russ)
University of Kazan, Kazan, 2015, 302 pp., ISBN 978-5-00019-442-3

T.I. Madzhidov, I.I. Baskin, and A.A. Varnek
Introduction into Chemoinformatics. Chemical Databases, (Russ)
University of Kazan, Kazan, 2015, 185 pp., ISBN 978-5-00019-429-4

T.I. Madzhidov, I.I. Baskin, I.A. Antipin and A.A. Varnek
Introduction into Chemoinformatics. Computer representation of chemical structures, (Russ)
University of Kazan, Kazan, 2013, 174 pp., ISBN 978-5-00019-131-6

Book Chapters

D. Horvath, G. Marcou and A. Varnek
Generative Topographic Approach to chemical space analysis
In "Challenges and advances in Computational Chemistry and Physics. v24, Advances in QSAR Modeling", 2017, 167-199

H.A. Gaspar, I.I. Baskin and A. Varnek
Visualize a Multidimensional Descriptor Space
In "Frontiers in Molecular Design and Chemical Information Science", 2016, ACS series book, 243-267

H.A. Gaspar, P. Sidorov, D. Horvath, I.I. Baskin, G. Marcou and A. Varnek
Generative Topographic Mapping Approach to Chemical Space Analysis
In "Frontiers in Molecular Design and Chemical Information Science", 2016, ACS series book, 212-241

G. Marcou and I.I. Baskin
Using Chemoinformatics Tools from R
In "Data Mining in Drug Discovery", 2014, Edited by Hoffmann RD; Gohier A; Pospisil P, Wiley-VCH, 179-208

I.I. Baskin and A. Varnek
Building a chemical space based on fragment descriptors
In "Advances in Combinatorial Chemistry & High Throughput Screening", 2014 Bentham Science Publishers, Rathnam Chaguturu, Ed., pp.36-59, ISBN: 978-1-60805-746-7

A. Varnek
Fragment Descriptors in Structure-Property Modeling and Virtual Screening.
In "Methods in molecular biology" (Clifton, N.J.) 2011, Vol:672, 213-43

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

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

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