Sitemap and docking
Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock […]
Grid generation 1-2
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Validate parameters 1-3
Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an […]
Binding Pose Metadynamics
Various binding configurations of a single ligand in a single binding site are ranked.
Shape screening 1-3
Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the […]
Docking 1
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]
Validate parameters 1
Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an […]
MCSS 1-2
Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list the compounds that aren't included in this […]
QM properties
Calculate molecular orbitals and vibrational frequencies. [Requires: Ligprep, Jaguar] [Keywords: quantum mechanics, semi-empirical, parameter flow […]