Build antibody 2
Several antibody models are built using Bioluminate starting from the heavy and light chain sequences. Sequences can be read from an XLS spreadsheet. […]
Database preparation 1-3
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.; […]
QM descriptors
It generates a series of jobs and harvests molecular (including Dipole Moment, HOMO/LUMO, isodensity surface contributions, Internal energy, energy […]
Shape 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 […]
Database preparation 1
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.; […]
Database 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 […]
QM Conformational search 1-3
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
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 […]
ESP 1
Run a semi-empirical and a Jaguar optimization job. Display the ligand ESP charges in Maestro. [Requires: LigPrep, Jaguar]