Class II-selective histone deacetylase inhibitors. Part 2: alignment-independent GRIND 3-D QSAR, homology and docking studies.
Ragno R, Simeoni S, Rotili D, Caroli A, Botta G, Brosch G, Massa S, Mai A, Eur J Med Chem, 2008 Mar - link

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.
Manetti F, Tintori C, Armand-Ugon M, Clotet-Codina I, Massa S, Ragno R, Este JA, Botta M, J Chem Inf Model, 2006 May-Jun - link

HIV-reverse transcriptase inhibition: inclusion of ligand-induced fit by cross-docking studies.
Ragno R, Frasca S, Manetti F, Brizzi A, Massa S, J Med Chem, 2005 Jan 13 - link

3-(4-Aroyl-1-methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamides as a new class of synthetic histone deacetylase inhibitors. 3. Discovery of novel lead compounds through structure-based drug design and docking studies.
Ragno R, Mai A, Massa S, Cerbara I, Valente S, Bottoni P, Scatena R, Jesacher F, Loidl P, Brosch G, J Med Chem, 2004 Mar 11 - link

3-(4-Aroyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-alkylamides as a new class of synthetic histone deacetylase inhibitors. 1. Design, synthesis, biological evaluation, and binding mode studies performed through three different docking procedures.
Mai A, Massa S, Ragno R, Cerbara I, Jesacher F, Loidl P, Brosch G, J Med Chem, 2003 Feb 13 - link

Investigation on QSAR and binding mode of a new class of human rhinovirus-14 inhibitors by CoMFA and docking experiments.
Artico M, Botta M, Corelli F, Mai A, Massa S, Ragno R, Bioorg Med Chem, 1996 Oct - link