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 […]
Epik
Predict ligand states with Epik and report the ionization form matrix. Generate with LigPrep minimized ionization-tautomeric forms ready to be […]
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 […]
AutoQSAR
Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR nodel to other compounds, with either traditional QSAR methods or […]
FEP analysis 1
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
Docking 1
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 […]
Protocol workflow
This workflow is used in the LiveDesign protocol. [Requires: LiveDesign]