MM 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 […]
Protonation forms
Protonation forms in LiveDesign Generate protonation forms with Epik and populates the LiveReport with the structure of the most probable form in a new […]
Database 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.; […]
Bioisoster replacement
Functional groups are replaced with bioisosteres that are available in the literature. [Requires: Maestro]
Bioluminate 1-4
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 […]
Split multimers 1
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Docking 1-2
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 […]
P450 SOM
In this workflow P450 Site of Metabolism calculation can be set and run to evaluate a set of ligands for the likely sites of metabolism by 2D6 or 2C9 P450 […]