IconLigand 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 […]

IconSemiempirical 

Run semi-empirical NDDO quantum chemical optimization and generate surface properties [Requires: Maestro, LigPrep]

IconFEP 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 […]

IconVirtual screening 1-3 

Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]

IconGrid 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 […]

IconParameter 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, […]

IconSitemap 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 […]

IconShape 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 […]

IconRun PyMOL 1-2 

Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]