A Combination of Molecular Dynamics and Docking Calculations to Explore the Binding Mode of ADS-J1, a Polyanionic Compound Endowed with Anti-HIV-1 Activity. - Fabrizio Manetti; Cristina Tintori; Mercedes Armand-Ugón; Imma Clotet-Codina; Silvio Massa; Rino Ragno; José A. Esté; Maurizio Botta (J. Chem. Inf. Model., 2006)

3-D QSAR Studies on Histone Deacetylase Inhibitors. A GOLPE/GRID Approach on Different Series of Compounds. - Rino Ragno; Silvia Simeoni; Sergio Valente; Silvio Massa; Antonello Mai (J. Chem. Inf. Model., 2006)

Small-Molecule Interferon Inducers. Toward the Comprehension of the Molecular Determinants through Ligand-Based Approaches. - Ira Musmuca; Silvia Simeoni; Antonia Caroli; Rino Ragno (J. Chem. Inf. Model., 2009)

Combining 3-D Quantitative Structure-Activity Relationship with Ligand Based and Structure Based Alignment Procedures for in Silico Screening of New Hepatitis C Virus NS5B Polymerase Inhibitors. - Ira Musmuca; Antonia Caroli; Antonello Mai; Neerja Kaushik-Basu; Payal Arora; Rino Ragno (J. Chem. Inf. Model., 2010)

Comprehensive model of wild-type and mutant HIV-1 reverse transciptases. - Flavio Ballante; Ira Musmuca; Garland R. Marshall; Rino Ragno (J. Comput. Aided Mol. Des., 2012)

3-D QSAutogrid/R: An Alternative Procedure To Build 3-D QSAR Models. Methodologies and Applications. - Flavio Ballante; Rino Ragno (J. Chem. Inf. Model., 2012)

Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. - Laura Silvestri; Flavio Ballante; Antonello Mai; Garland R. Marshall; Rino Ragno (J. Chem. Inf. Model., 2012)

Pharmacophore Assessment Through 3-D QSAR: Evaluation of the Predictive Ability on New Derivatives by the Application on a Series of Antitubercular Agents. - Laura Friggeri; Flavio Ballante; Rino Ragno; Ira Musmuca; Daniela de Vita; Fabrizio Manetti; Mariangela Biava; Luigi Scipione; Roberto Di Santo; Roberta Costi; Marta Feroci; Silvano Tortorella (J. Chem. Inf. Model., 2013)

Hsp90 Inhibitors, Part 1: Definition of 3-D QSAutogrid/R Models as a Tool for Virtual Screening. - Flavio Ballante; Antonia Caroli; Richard B. Wickersham III; Rino Ragno (J. Chem. Inf. Model., 2014)

Hsp90 Inhibitors, Part 2: Combining Ligand-Based and Structure-Based Approaches for Virtual Screening Application. - Antonia Caroli; Flavio Ballante; Richard B. Wickersham III; Federico Corelli; Rino Ragno (J. Chem. Inf. Model., 2014)

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches. - Rino Ragno; Flavio Ballante; Adele Pirolli; Richard B. Wickersham III; Alexandros Patsilinakos; Stéphanie Hesse; Enrico Perspicace; Gilbert Kirsch (J. Comput. Aided Mol. Des., 2015)

Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H-Chromen-2-One Core: Structure-Based and Ligand-Based Derived Three-Dimensional Quantitative Structure-Activity Relationships Predictive Models. - Milan Mladenovic; Alexandros Patsilinakos; Adele Pirolli; Manuela Sabatino; Rino Ragno (J. Chem. Inf. Model., 2017)

Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. - Manuela Sabatino; Dante Rotili; Alexandros Patsilinakos; Mariantonietta Forgione; Daniela Tomaselli; Fréderic Alby; Paola B. Arimondo; Antonello Mai; Rino Ragno (J. Comput. Aided Mol. Des., 2018)

www.3d-qsar.com: a web portal that brings 3-D QSAR to all electronic devices - the Py-CoMFA web application as tool to build models from pre-aligned datasets. - Rino Ragno (J. Comput. Aided Mol. Des., 2019)

Human Estrogen Receptor α Antagonists. Part 1: 3-D QSAR-Driven Rational Design of Innovative Coumarin-Related Antiestrogens as Breast Cancer Suppressants through Structure-Based and Ligand-Based Studies. - Nezrina Mihovic; Nevena Tomasevic; Sanja Matic; Marina M. Mitrovic; Danijela A. Kostic; Manuela Sabatino; Lorenzo Antonini; Rino Ragno; Milan Mladenovic (J. Chem. Inf. Model., 2021)

Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal. - Eleonora Proia; Alessio Ragno; Lorenzo Antonini; Manuela Sabatino; Milan Mladenovic; Roberto Capobianco; Rino Ragno (J. Comput. Aided Mol. Des., 2022)

Bovine Serum Amine Oxidase and Polyamine Analogues: Chemical Synthesis and Biological Evaluation Integrated with Molecular Docking and 3-D QSAR Studies. - Rino Ragno; Anna Minarini; Eleonora Proia; Lorenzo Antonini; Andrea Milelli; Vincenzo Tumiatti; Marco Fiore 003; Pasquale Fino; Lavinia Rutigliano; Rossella Fioravanti; Tomoaki Tahara; Elena Pacella; et al. (J. Chem. Inf. Model., 2022)

Explainable AI in drug discovery: self-interpretable graph neural network for molecular property prediction using concept whitening. - Michela Proietti; Alessio Ragno; Biagio La Rosa; Rino Ragno; Roberto Capobianco (Mach. Learn., 2024)

Essential Oils as Antimicrobials against Acinetobacter baumannii: Experimental and Literature Data to Definite Predictive Quantitative Composition-Activity Relationship Models Using Machine Learning Algorithms. - Roberta Astolfi; Alessandra Oliva; Antonio Raffo; Filippo Sapienza; Alessio Ragno; Eleonora Proia; Claudio M. Mastroianni; Cristina Luceri; Mijat Bozovic; Milan Mladenovic; Rosanna Papa; Patrizia Bottoni; et al. (J. Chem. Inf. Model., 2025)