Ligand alignment MD refinement 1
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Split multimers 1-3
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Semiempirical
Run semi-empirical NDDO quantum chemical optimization and generate surface properties [Requires: Maestro, LigPrep]
FEP analysis 2
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
Virtual screening 1-3
Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]
Grid generation 1
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Parameter flow variables 1
Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the protein preparation, […]
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 […]
Shape screening 1-2
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 […]
Run PyMOL 1-2
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]