Bioisosteres
Bioisosteres - in LiveDesign Replace functional groups of each LiveReport ligand with bioisosteres, generating all the single replacements. The […]
Protein Alignment
Extract one monomer from each of the two multimers. Align the binding sites (via the 'Align Binding Sites' node) or the whole structure (using the 'Protein […]
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 […]
Bioluminate 1-2
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 […]
MM Conformational search 1
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Split multimers 1-2
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 […]
Unpivot
Use a loop to unpivot the data. See also the Similarity search workflow example where the Unpivot node is used instead. See also the Cheminformatics > […]
Jobcontrol 1-2
The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It […]
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 […]