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. […]
Split multimers 1
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Validate parameters 1-2
Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an […]
Bioisosteres
Bioisosteres - in LiveDesign Replace functional groups of each LiveReport ligand with bioisosteres, generating all the single replacements. The […]
MM 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 […]
Diversity
Pick diverse molecules from a library and inspect the structures. [Requires: Canvas]
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 […]
MD simulation 1
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
KNIME Server - QikProp
Workflow to be run on a KNIME server and invoked from a LiveDesign Computational model. [Requires: LigPrep, QikProp]