Db Main.mdb Yahoo.rar

[Franha Pec]

The 3D structures of the compounds had been sketched and energy minimisation subsequently using the graphical user interface (GUI) of the MOE software [24] running on a Linux workstation with a 3.5GHz Intel Core2 Duo processor. The 3D structures were generated using the builder module of MOE and energy minimization was subsequently carried out using the MMFF94 force field [25] until a gradient of 0.01 kcal/mol was reached. The 3D structures of the compounds were then saved as.mol2 files subsequently included into a MOE database (.mdb) file and converted to other file formats (.sdf,.mol,.mol2 and.ldb), which are suitable for use in several virtual screening workflow protocols. The molar weight (MW), number of rotatable bonds (NRB), lipophilicity parameter (log P), number of hydrogen bond acceptors (HBA), number of hydrogen bond donors (HBD) and number of Lipinski violations were calculated using the molecular descriptor calculator included in the QuSAR module of the MOE package [24]. A further treatment was carried out to ensure that the protanation states of the compounds were correct with respect to biological pH (strong acids were deprotonated, strong bases protonated and metal atoms removed). A maximum of 10 tautomers were generated for each molecule in the dataset.

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