IconMM Conformational search 1-3 

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

IconRun Maestro, command 

Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro and use this selection to build an […]

IconPython script 1-2 

The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between […]

IconDiversity 

Pick diverse molecules from a library and inspect the structures. [Requires: Canvas]

IconCovalent docking 

Dock and covalently binds ligands to the specified reactive residue in the protein target using Michael addition reaction type. [Requires: ProteinPrep, […]

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 […]

IconDatabase analysis 1-2 

Assess the coverage of a database from the distribution of the distance to the nearest neighbor of each molecule in the database. List the three most […]

IconClustering 1 

Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]

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 […]