Molecular docking and spatial coarse graining simulations as tools to investigate substrate recognition, enhancer binding and conformational transitions in indoleamine-2,3-dioxygenase (IDO).
Macchiarulo A, Nuti R, Bellocchi D, Camaioni E, Pellicciari R, Biochim Biophys Acta, 2007 Aug - link

Synthesis, docking studies and anti-inflammatory activity of 4,5,6,7-tetrahydro-2H-indazole derivatives.
Rosati O, Curini M, Marcotullio MC, Macchiarulo A, Perfumi M, Mattioli L, Rismondo F, Cravotto G, Bioorg Med Chem, 2007 May 15 - link

Docking studies on PARP-1 inhibitors: insights into the role of a binding pocket water molecule.
Bellocchi D, Macchiarulo A, Costantino G, Pellicciari R, Bioorg Med Chem, 2005 Feb 15 - link

Insights into phenylalanine derivatives recognition of VLA-4 integrin: from a pharmacophoric study to 3D-QSAR and molecular docking analyses.
Macchiarulo A, Costantino G, Meniconi M, Pleban K, Ecker G, Bellocchi D, Pellicciari R, J Chem Inf Comput Sci, 2004 Sep-Oct - link

1,4-Benzothiazine and 1,4-benzoxazine imidazole derivatives with antifungal activity: a docking study.
Macchiarulo A, Costantino G, Fringuelli D, Vecchiarelli A, Schiaffella F, Fringuelli R, Bioorg Med Chem, 2002 Nov - link

Modeling of poly(ADP-ribose)polymerase (PARP) inhibitors. Docking of ligands and quantitative structure-activity relationship analysis.
Costantino G, Macchiarulo A, Camaioni E, Pellicciari R, J Med Chem, 2001 Nov 8 - link