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 […]
Docking 1-3
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]
Reaction-based enumeration
Enumerate structures by substitution of R groups in the reactants and products of a single- or multi-step reaction. It is also use for Core hopping.
Ligand 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 […]
KNIME Server - QikProp
Workflow to be run on a KNIME server and invoked from a LiveDesign Computational model. [Requires: LigPrep, QikProp]
Covalent docking
Dock and covalently binds ligands to the specified reactive residue in the protein target using Michael addition reaction type. [Requires: ProteinPrep, […]
ESP 1
Run a semi-empirical and a Jaguar optimization job. Display the ligand ESP charges in Maestro. [Requires: LigPrep, Jaguar]
Build antibody 1
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.; […]
Bioluminate 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 […]