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Glide standard precision molecular docking

SD Suresh Dharuman
LW Laura A. Wilt
JL Jiuyu Liu
SR Stephanie M. Reeve
CT Carl W. Thompson
JE John M. Elmore
DS Dimitri Shcherbakov
RL Robin B. Lee
EB Erik C. Böttger
RL Richard E. Lee
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All conformations generated from LigPrep were docked using Schrödinger’s Glide program [33–35]. Ligand sampling was flexible, and docked conformers were required to match at least one hydrogen bonding interaction from the constraints generated in the receptor grid. To soften the potential for nonpolar parts of the ligands, van der Waals (VDW) radii were scaled using a scaling factor of 0.80 for ligand atoms with a partial charge < 0.15 (default Glide settings). Post-docking minimization was performed on all poses generated by Glide using the OPLS3 force field prior to the assignment of Glide docking scores. Ligand poses with the highest ranked Glide scores were used to evaluate binding. The highest ranked analogs, 1 (spectinomycin), 2, 5, 6, 9, and 10, were advanced to molecular dynamics simulations.

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