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Organic & Biomolecular Chemistry
DOI: 10.1039/C6OB01003B
prepared templates. The best 100 models were selected based on
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a normalized DOPE score. All structures produced had a perfect
GA341 score of 1.0. The chosen models were then clustered
using the Calibur68 program and the most representative structure
of the largest cluster was chosen as the final homology model.
Ligands were drawn using the SybylX program and subjected to a
minimization stage by using the MMFF force field using the
BFGS algorithm in 1000 steps or until energy conversion
(grad=0.1).
10 Molecular docking simulations were run using the Autodock
Vina69 software using the default scoring function weights and an
optimized exhaustiveness parameter of 16. For each ligand, 20
different poses were produced. The search space had the
following dimensions x*y*z=29*24*28= 19488 Å3 centered
15 around the active site region.
55
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This work has been partially supported by the Labex SynOrg
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