IconDatabase analysis 1 

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 […]

IconQM descriptors 

It generates a series of jobs and harvests molecular (including Dipole Moment, HOMO/LUMO, isodensity surface contributions, Internal energy, energy […]

IconBioluminate 1-3 

The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the […]

IconLiveDesign 1 

Structures and properties are retrieved from Live Design. New properties are added to an existing Live report. [Products: Live Design]

IconReactive protein residues 

Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures. [Requires: […]

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 […]

IconShape 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 […]

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 […]