IconReaders and Writers 

Read and write structure files. Read a list of PDB files from a directory. [Requires: Maestro] See also: - Docking - Grid generation: Glide grid […]

IconDatabase preparation 1-2 

Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]

IconMM Conformational search 1-4 

Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]

IconGroupBy 1-2 

Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]

IconShape screening 1-4 

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 […]

IconQM properties 

Calculate molecular orbitals and vibrational frequencies. [Requires: Ligprep, Jaguar] [Keywords: quantum mechanics, semi-empirical, parameter flow […]