Molecular operating environment moe 2015

Molecular modeling experiments were performed using the Molecular Operating Environment MOE 2015.10 from Chemical Computing Group (Montreal, QC, Canada). Co-crystal structures of MMP-7 are available from the Protein Data Bank. For the actual work PDB code: 2Y6D was selected for the computational studies. In MOE the pocket was prepared for the dockings via the Protonate 3D method applying the default values for temperature 300 K, pH 7 and salt 0.1. The ligands to be docked to the protein were imported from SD files to receive a MOE compatible molecular database. As the SD files did not contain 3D coordinates, they were generated directly using MOE rebuild3D with an RMSD gradient of 0.1. For docking experiments the Amber10:EHT force field [46 (link),47 (link)] was used. The triangle matcher placement was applied with a rigid receptor. The docked poses were subsequently analyzed with respect to their scores and interactions with the target enzyme.

Molecular modelling experiments were performed using the Molecular Operating Environment MOE 2015.10 from Chemical Computing Group. Co-crystal structures of GP are available from the Protein Data Bank. For the actual work pdb entry: 3G2N was selected for the computational studies. In MOE the pocket was prepared for the dockings via the Protonate 3D method applying the default values for temperature 300 K, pH 7 and salt 0.1. The ligands to be docked to the protein were imported from SD files to receive a MOE compatible molecular database. As the SD files did not contain 3D coordinates, they were generated directly using MOE rebuild3D with an RMSD gradient of 0.1. For docking experiments the Amber10:EHT force field was used [23 (link),24 (link)]. The pharmacophore placement was applied with a rigid receptor. The docked poses were subsequently analysed with respect to their scores and interactions with the target enzyme.