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were enclosed.
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ical method AM1. The AutoDockTools was used to
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(
c) Vigorita, M. G.; Previtera, T.; Ottan a` , R.; Grillone, I.;
7
.3.2. Docking calculations. Docking studies to COX-2
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were carried out using the package AutoDock 3.0, a pro-
gram that allows torsional flexibility in the ligand, while
the protein is kept rigid. The grid spacing was 0.375 A
in each dimension, and each grid map consists of
1
8
˚
6
0 · 60 · 60 grid points. The grid was centered on the
selective site, using the SC-558 crystallographic position
as reference. The AutoGrid program generated separate
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one for electrostatic interactions. We used the so-called
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method. For both ligands, each LCG job consists of
1
1
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position and orientation chosen randomly. The binding
00 independent runs, starting each time from a different
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˚
modes were clustered using rmsd cutoff of 1.0 A with re-
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used as default settings and the results were ranked by
the lowest energy representative of each cluster com-
bined with the root mean square deviation.
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Acknowledgment
1
6. Bruno, G.; Costantino, L.; Curinga, C.; Maccari, R.;
Monforte, F.; Nicol o` , F.; Ottan a` , R.; Vigorita, M. G.
Bioorg. Med. Chem. 2002, 10, 1077–1084.
This work was financially supported by the Fondo
Ateneo di Ricerca (University of Messina, Italy).
1
7. Abdel-Salam, O. M. E.; Baiuomy, A. R.; Arbid, M. S.
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