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-10 M. The solvent was removed and the receptor sequences were aligned and superimposed considering the binding pockets residues (RMSD = 0.25). The pharmacophore model was created using the PPCH-ALL (Planar-Polarity-Charge-Hydrophobicity) scheme. Consensus parameters: Tolerance = 1.1; Threshold = 50%. As spatial constraints were created a volume exclusion feature using the binding pocket of pdb 2NNO complex.
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21
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85043080901
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note
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Virtual screening procedures. The ZINC lead-like database was washed using the appropriate function implemented in MOE. Next, the database compounds were filtered with the docking function of MOE (parameters: derived four-point pharmacophore; Placement = Alpha Triangle; Rescoring = London dG). The hits were partitioned into two different databases (containing and non-containing sulfo groups). The structures without S groups were filtered by FlexX docking program (all parameters were kept as default).
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22
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26 Mass-centered grid maps were generated with 80 grid points for every direction and with 0.375 Angstroms spacing by the AutoGrid program for the whole protein target. Random starting position on the entire protein surface, random orientations and torsions were used for the ligands. The distance-dependent dielectric permittivity of Mehler and Solmajer was used for the calculation of the electrostatic grid-maps. One hundred independent docking runs were carried out for each ligand. The cluster analyses were computed with a cluster tolerance by less than 1.5 in positional root-mean-square deviation with AutoDock Tools.
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24
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85043043136
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note
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8 represent the means from at least three different determinations.
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25
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