MCSS 1-4
Maximum Common Substructure Search (MCS): Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list […]
Similarity 1-2
Find the most similar compounds to a sketched molecule in a database. Screen the same database against several query structures. [Requires: Canvas]
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 […]
Substructure 1-2
Search a set of structures against a sketched query molecule or SMARTS patterns. Report the compounds that don't pass all the REOS filters. [Requires: […]
Ensemble docking
Ensemble docking in LiveDesign Ensemble docking in 2 binding site conformations and the best scoring conformation is reported along with the […]
MD simulation 1-2
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
Job control
Schrodinger Job control
Shape screening 1-5
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 […]
Clustering 1-4
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
MM Conformational search 1-2
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]