Vanilla Glide
Maestro 2016-3
Glide 7.2
Glide default ligand pose generation
GlideSP scoring function
Maximum number of ligand poses=5
VDW scaling factor=0.8
Glide Default ligand sampling
All 102 ligands were docked to each of the four structures using GLIDE SP with default parameters. The top score for each ligand was used for this submission.
Vanilla Glide
Maestro 2016-3
Glide 7.2
pH 7.4
Tautomers considered
OPLS2005 Forcefield
The work for this submission has been performed by the following people:
Steven Ramsey, Tom Kurtzman; Lehman College of CUNY
Emilio Gallicchio; Brooklyn College of CUNY
Lauren Wickstrom; Borough of Manhattan Community College of CUNY
Identification of Target Structures - To address the significant loop and helical reorganization, A subset of four protein structures from the 36 provided were identified to be used for docking. These four (structure ids: hgaf, nqqw, hqmf, fggu) were chosen by first grouping ligands into four groups (+1 outlier group) with common core features and picking a representative structure from each group.
Each of the four structures was protonated with the ligand and crystallographic water molecules in place using Maestro's prepwizard with default parameter settings. Protonation states were visually inspected with particular attention paid to HIS, ASN, and GLN. HIS451 and 298 protonation states and/or flip state were modified in each of the four structures to best maintain local hydrogen bond contacts.
Ligprep was used to prepare the ligands with
all default settings except that core positions were maintained.
Glide default ligand pose generation
GlideSP scoring function
Maximum number of ligand poses=5
VDW scaling factor=0.8
Glide Default ligand sampling
All 102 ligands were docked to each of the four structures using GLIDE SP with default parameters. The top score for each ligand was used for this submission.