Molecular Topology, 15. 3D Distance Matrixes and Related Topological Indices. - Mircea V. Diudea; Dragos Horvath; Ante Graovac (J. Chem. Inf. Comput. Sci., 1995)

Reactivity Prediction Models Applied to the Selection of Novel Candidate Building Blocks for High-Throughput Organic Synthesis of Combinatorial Libraries. - Mircea Braban; Iuliana Pop; Xavier Willard; Dragos Horvath (J. Chem. Inf. Comput. Sci., 1999)

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. - Dragos Horvath; Catherine Jeandenans (J. Chem. Inf. Comput. Sci., 2003)

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. - Dragos Horvath; Catherine Jeandenans (J. Chem. Inf. Comput. Sci., 2003)

Fuzzy Tricentric Pharmacophore Fingerprints, 1. Topological Fuzzy Pharmacophore Triplets and Adapted Molecular Similarity Scoring Schemes. - Fanny Bonachéra; Benjamin Parent; Frédérique Barbosa; Nicolas Froloff; Dragos Horvath (J. Chem. Inf. Model., 2006)

Grid-based evolutionary strategies applied to the conformational sampling problem. - Benjamin Parent; Alexandru-Adrian Tantar; Nouredine Melab; El-Ghazali Talbi; Dragos Horvath (IEEE Congress on Evolutionary Computation, 2007)

A parallel hybrid genetic algorithm for protein structure prediction on the computational grid. - Alexandru-Adrian Tantar; Nouredine Melab; El-Ghazali Talbi; Benjamin Parent; Dragos Horvath (Future Gener. Comput. Syst., 2007)

Stochastic versus Stepwise Strategies for Quantitative Structure-Activity Relationship GenerationHow Much Effort May the Mining for Successful QSAR Models Take? - Dragos Horvath; Fanny Bonachéra; Vitaly P. Solov'ev; Cédric Gaudin; Alexandre Varnek (J. Chem. Inf. Model., 2007)

Optimized Evolutionary Strategies in Conformational Sampling. - Benjamin Parent; Annemarie M. Kökösy; Dragos Horvath (Soft Comput., 2007)

Parallel multi-objective algorithms for the molecular docking problem. - Jean-Charles Boisson; Laetitia Jourdan; El-Ghazali Talbi; Dragos Horvath (CIBCB, 2008)

Fuzzy Tricentric Pharmacophore Fingerprints. 2. Application of Topological Fuzzy Pharmacophore Triplets in Quantitative Structure-Activity Relationships. - Fanny Bonachéra; Dragos Horvath (J. Chem. Inf. Model., 2008)

Local vs. global search strategies in evolutionary GRID-based conformational sampling & docking. - Dragos Horvath; Lorraine Brillet; S. Roy; Sébastien Conilleau; Alexandru-Adrian Tantar; Jean-Charles Boisson; Nouredine Melab; El-Ghazali Talbi (IEEE Congress on Evolutionary Computation, 2009)

Predicting the Predictability: A Unified Approach to the Applicability Domain Problem of QSAR Models. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2009)

Simplified chain folding models as metaheuristic benchmark for tuning real protein folding algorithms? - Dragos Horvath; Camelia Chira (IEEE Congress on Evolutionary Computation, 2010)

An Evolutionary Model Based on Hill-Climbing Search Operators for Protein Structure Prediction. - Camelia Chira; Dragos Horvath; Dumitru Dumitrescu (EvoBIO, 2010)

A unified approach to the applicability domain problem of QSAR models. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Cheminformatics, 2010)

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set. - Iurii Sushko; Sergii Novotarskyi; Robert Körner; Anil Kumar Pandey; Artem Cherkasov; Jiazhong Li; Paola Gramatica; Katja Hansen; Timon Schroeter; Klaus-Robert Müller; Lili Xi; Huanxiang Liu; et al. (J. Chem. Inf. Model., 2010)

Single- and Multi-Objective Cooperation for the Flexible Docking Problem. - Jean-Charles Boisson; Laetitia Jourdan; El-Ghazali Talbi; Dragos Horvath (J. Math. Model. Algorithms, 2010)

Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction. - Camelia Chira; Dragos Horvath; D. Dumitrescu (BioData Min., 2011)

Local neighborhood behavior in a combinatorial library context. - Dragos Horvath; Christian J. Koch; Gisbert Schneider; Gilles Marcou; Alexandre Varnek (J. Comput. Aided Mol. Des., 2011)

Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches. - Aurélie de Luca; Dragos Horvath; Gilles Marcou; Vitaly P. Solov'ev; Alexandre Varnek (J. Chem. Inf. Model., 2012)

Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms. - Christophe Muller; Gilles Marcou; Dragos Horvath; João Aires-de-Sousa; Alexandre Varnek (J. Chem. Inf. Model., 2012)

Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS). - Héléna A. Gaspar; Gilles Marcou; Dragos Horvath; Alban Arrault; Sylvain Lozano; Philippe Vayer; Alexandre Varnek (J. Chem. Inf. Model., 2013)

S4MPLE - Sampler For Multiple Protein-Ligand Entities: Simultaneous Docking of Several Entities. - Laurent Hoffer; Dragos Horvath (J. Chem. Inf. Model., 2013)

In Silico Fragment-Based Drug Discovery: Setup and Validation of a Fragment-to-Lead Computational Protocol Using S4MPLE. - Laurent Hoffer; Jean-Paul Renaud; Dragos Horvath (J. Chem. Inf. Model., 2013)

Do Not Hesitate to Use Tversky - and Other Hints for Successful Active Analogue Searches with Feature Count Descriptors. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2013)

Computational chemogenomics: Is it more than inductive transfer? - J. B. Brown; Yasushi Okuno; Gilles Marcou; Alexandre Varnek; Dragos Horvath (J. Comput. Aided Mol. Des., 2014)

Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds. - Pavel Sidorov; Héléna A. Gaspar; Gilles Marcou; Alexandre Varnek; Dragos Horvath (J. Comput. Aided Mol. Des., 2015)

Chemical Data Visualization and Analysis with Incremental Generative Topographic Mapping: Big Data Challenge. - Héléna A. Gaspar; Igor I. Baskin; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2015)

Stargate GTM: Bridging Descriptor and Activity Spaces. - Héléna A. Gaspar; Igor I. Baskin; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2015)

Expert System for Predicting Reaction Conditions: The Michael Reaction Case. - Gilles Marcou; João Aires-de-Sousa; Diogo A. R. S. Latino; Aurélie de Luca; Dragos Horvath; V. Rietsch; Alexandre Varnek (J. Chem. Inf. Model., 2015)

Prediction of Activity Cliffs Using Condensed Graphs of Reaction Representations, Descriptor Recombination, Support Vector Machine Classification, and Support Vector Regression. - Dragos Horvath; Gilles Marcou; Alexandre Varnek; Shilva Kayastha; Antonio de la Vega de León; Jürgen Bajorath (J. Chem. Inf. Model., 2016)

Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set. - Kyrylo Klimenko; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2016)

Kernel Target Alignment Parameter: A New Modelability Measure for Regression Tasks. - Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Chem. Inf. Model., 2016)

From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets. - Shilva Kayastha; Ryo Kunimoto; Dragos Horvath; Alexandre Varnek; Jürgen Bajorath (J. Comput. Aided Mol. Des., 2017)

QSAR modeling and chemical space analysis of antimalarial compounds. - Pavel Sidorov; Birgit Viira; Elisabeth Davioud-Charvet; Uko Maran; Gilles Marcou; Dragos Horvath; Alexandre Varnek (J. Comput. Aided Mol. Des., 2017)

Privileged Structural Motif Detection and Analysis Using Generative Topographic Maps. - Shilva Kayastha; Dragos Horvath; Erik Gilberg; Michael Gütschow; Jürgen Bajorath; Alexandre Varnek (J. Chem. Inf. Model., 2017)

Rescoring of docking poses under Occam's Razor: are there simpler solutions? - Michael Zhenin; Malkeet Singh Bahia; Gilles Marcou; Alexandre Varnek; Hanoch Senderowitz; Dragos Horvath (J. Comput. Aided Mol. Des., 2018)

Multi-task generative topographic mapping in virtual screening. - Arkadii I. Lin; Dragos Horvath; Gilles Marcou; Bernd Beck; Alexandre Varnek (J. Comput. Aided Mol. Des., 2019)

Virtual Screening with Generative Topographic Maps: How Many Maps Are Required? - Iuri Casciuc; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Jürgen Bajorath; Alexandre Varnek (J. Chem. Inf. Model., 2019)

CovaDOTS: In Silico Chemistry-Driven Tool to Design Covalent Inhibitors Using a Linking Strategy. - Laurent Hoffer; Magali Saez-Ayala; Dragos Horvath; Alexandre Varnek; Xavier Morelli; Philippe Roche (J. Chem. Inf. Model., 2019)

De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping. - Boris Sattarov; Igor I. Baskin; Dragos Horvath; Gilles Marcou; Esben Jannik Bjerrum; Alexandre Varnek (J. Chem. Inf. Model., 2019)

Diversifying chemical libraries with generative topographic mapping. - Arkadii I. Lin; Bernd Beck; Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Comput. Aided Mol. Des., 2020)

"Big Data" Fast Chemoinformatics Model to Predict Generalized Born Radius and Solvent Accessibility as a Function of Geometry. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2020)

Trustworthiness, the Key to Grid-Based Map-Driven Predictive Model Enhancement and Applicability Domain Control. - Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2020)

Chemography: Searching for Hidden Treasures. - Yuliana Zabolotna; Arkadii I. Lin; Dragos Horvath; Gilles Marcou; Dmitriy M. Volochnyuk; Alexandre Varnek (J. Chem. Inf. Model., 2021)

HIV-1 drug resistance profiling using amino acid sequence space cartography. - Karina Pikalyova; Alexey Orlov; Arkadii I. Lin; Olga A. Tarasova; Gilles Marcou; Dragos Horvath; Vladimir Poroikov; Alexandre Varnek (Bioinform., 2022)

Inverse QSAR: Reversing Descriptor-Driven Prediction Pipeline Using Attention-Based Conditional Variational Autoencoder. - William Bort; Daniyar Mazitov; Dragos Horvath; Fanny Bonachéra; Arkadii I. Lin; Gilles Marcou; Igor I. Baskin; Timur I. Madzhidov; Alexandre Varnek (J. Chem. Inf. Model., 2022)

Chemspace Atlas: Multiscale Chemography of Ultralarge Libraries for Drug Discovery. - Yuliana Zabolotna; Fanny Bonachéra; Dragos Horvath; Arkadii I. Lin; Gilles Marcou; Olga Klimchuk; Alexandre Varnek (J. Chem. Inf. Model., 2022)

SynthI: A New Open-Source Tool for Synthon-Based Library Design. - Yuliana Zabolotna; Dmitriy M. Volochnyuk; Sergey V. Ryabukhin; Kostiantyn Gavrylenko; Dragos Horvath; Olga Klimchuk; Oleksandr Oksiuta; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2022)

A Close-up Look at the Chemical Space of Commercially Available Building Blocks for Medicinal Chemistry. - Yuliana Zabolotna; Dmitriy M. Volochnyuk; Sergey V. Ryabukhin; Dragos Horvath; Konstantin S. Gavrilenko; Gilles Marcou; Yurii S. Moroz; Oleksandr Oksiuta; Alexandre Varnek (J. Chem. Inf. Model., 2022)

Chemical Library Space: Definition and DNA-Encoded Library Comparison Study Case. - Regina Pikalyova; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2023)

GENERA: A Combined Genetic/Deep-Learning Algorithm for Multiobjective Target-Oriented De Novo Design. - Giuseppe Lamanna; Pietro Delre; Gilles Marcou; Michele Saviano; Alexandre Varnek; Dragos Horvath; Giuseppe Felice Mangiatordi (J. Chem. Inf. Model., 2023)

Meta-GTM: Visualization and Analysis of the Chemical Library Space. - Regina Pikalyova; Yuliana Zabolotna; Dragos Horvath; Gilles Marcou; Alexandre Varnek (J. Chem. Inf. Model., 2023)

Combinatorial Library Neural Network (CoLiNN) for Combinatorial Library Visualization Without Compound Enumeration. - Regina Pikalyova; Tagir Akhmetshin; Dragos Horvath; Alexandre Varnek (ICANN (10), 2024)

De Novo Drug Design - Do We Really Want to Be "Original"? - A Real-world Case Study on Colchicine-Site Tubulin Binders. - Maxim Shevelev; Dragos Horvath; Gilles Marcou; Alexandre Varnek (ICANN (10), 2024)

Higher education in chemoinformatics: achievements and challenges. - Alexandre Varnek; Gilles Marcou; Dragos Horvath (J. Cheminformatics, 2025)