A quasi-flexible automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation. - Stefano Alcaro; Francesco Gasparrini; O. Incani; S. Mecucci; D. Misiti; Marco Pierini; Claudio Villani (J. Comput. Chem., 2000)

Molecular Modeling of DNA Cross-linking Analogues Based on the Azinomycin Scaffold. - Stefano Alcaro; Francesco Ortuso; Robert S. Coleman (J. Chem. Inf. Model., 2005)

GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition. - Francesco Ortuso; Thierry Langer; Stefano Alcaro (Bioinform., 2006)

"Quasi flexible" automatic docking processing for studying stereoselective recognition mechanisms, part 2: Prediction of Delta Delta G of complexation and 1H-NMR NOE correlation. - Stefano Alcaro; Francesco Gasparrini; O. Incani; L. Caglioti; Marco Pierini; Claudio Villani (J. Comput. Chem., 2007)

Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1 Protease Complexed with Four Approved Drugs: Mechanism of Binding and Drug Resistance. - Stefano Alcaro; Anna Artese; Francesca Ceccherini-Silberstein; Francesco Ortuso; Carlo-Federico Perno; Tobias Sing; Valentina Svicher (J. Chem. Inf. Model., 2009)

Computer-Aided Molecular Design of Asymmetric Pyrazole Derivatives with Exceptional Enantioselective Recognition toward the Chiralcel OJ-H Stationary Phase. - Stefano Alcaro; Adriana Bolasco; Roberto Cirilli; Rosella Ferretti; Rossella Fioravanti; Francesco Ortuso (J. Chem. Inf. Model., 2012)

GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods. - Simon Cross; Francesco Ortuso; Massimo Baroni; Giosuè Costa; Simona Distinto; Federica Moraca; Stefano Alcaro; Gabriele Cruciani (J. Chem. Inf. Model., 2012)

Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. - Mengjie Chen; Valentina Svicher; Anna Artese; Giosuè Costa; Claudia Alteri; Francesco Ortuso; Lucia Parrotta; Yang Liu 007; Chang Liu; Carlo-Federico Perno; Stefano Alcaro; Jing Zhang 010 (Bioinform., 2013)

Antioxidant Efficiency of Oxovitisin, a New Class of Red Wine Pyranoanthocyanins, Revealed through Quantum Mechanical Investigations. - Stefano Alcaro; Sandro Giuseppe Chiodo; Monica Leopoldini; Francesco Ortuso (J. Chem. Inf. Model., 2013)

In Silico Identification and Biological Evaluation of Novel Selective Serum/Glucocorticoid-Inducible Kinase 1 Inhibitors Based on the Pyrazolo-Pyrimidine Scaffold. - Francesco Ortuso; Rosario Amato; Anna Artese; Lucia D'antona; Giosuè Costa; Cristina Talarico; Francesco Gigliotti; Cataldo Bianco; Francesco Trapasso; Silvia Schenone; Francesca Musumeci; Lorenzo Botta; et al. (J. Chem. Inf. Model., 2014)

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins. - Francesca Spyrakis; Paolo Benedetti; Sergio Decherchi; Walter Rocchia; Andrea Cavalli; Stefano Alcaro; Francesco Ortuso; Massimo Baroni; Gabriele Cruciani (J. Chem. Inf. Model., 2015)

G-quadruplex Structure Prediction and integration in the GenData2020 data model. - Giuseppe Tradigo; Francesca Cristiano; Stefano Alcaro; Sergio Greco; Gianluca Pollastri; Pierangelo Veltri; Mattia Prosperi (BCB, 2016)

Optimized Virtual Screening Workflow for the Identification of Novel G-Quadruplex Ligands. - Teresa Kaserer; Riccardo Rigo; Philipp Schuster; Stefano Alcaro; Claudia Sissi; Daniela Schuster 001 (J. Chem. Inf. Model., 2016)

Targeting SARS-CoV-2 Main Protease: A Successful Story Guided by an In Silico Drug Repurposing Approach. - Francesca Alessandra Ambrosio; Giosuè Costa; Isabella Romeo; Francesca Esposito; Mohammad Alkhatib; Romina Salpini; Valentina Svicher; Angela Corona; Paolo Malune; Enzo Tramontano; Francesca Ceccherini-Silberstein; Stefano Alcaro; et al. (J. Chem. Inf. Model., 2023)

Exploring Structural Requirements for Sigma-1 Receptor Linear Ligands: Experimental and Computational Approaches. - Lisa Lombardo; Salvatore Mirabile; Rosaria Gitto; Giuseppe Cosentino; Stefano Alcaro; Maria Dichiara; Agostino Marrazzo; Emanuele Amata; Francesco Ortuso; Laura De Luca (J. Chem. Inf. Model., 2024)