1) Protein Prep
Single receptor workflow
Folder chooser count may include hidden items; only receptor file types are ingested.
1a) Box Generation
Lig
Resi
Chain
Residue
Å
Detected HETATM ligands
1b) Protein Preparation (3a)
HETATM to remove
Open a receptor to populate…
Chains to remove
Open a receptor to populate…
Backend
AltLoc
queued…
1c) Preparation
Select HETATMs and chains to remove for each receptor:
queued…
1d) Review Prepared Receptor(s)
Prepared receptor preview
Inspect the generated PDBQT output before moving on to ligands.
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2) Ligand Prep
Or start from a curated ChEMBL drug list
These preset CSV libraries are useful when a user does not already have ligands in mind.
Phase 2 or higher means the compounds reached clinical testing and were not immediately ruled out as lethally unsafe in that context,
but that does not mean they are non-toxic or safe for every purpose, dose, tissue, or patient population.
CSV column mapping
Required for CSV ligand input.
Optional if your CSV has no identifier column.
3) Build Job Package
Joey Pegasus mode uses brd on gpu_cheminfo (16 CPUs; Vina 240:00, ConfGen 48:00). The ZIP includes these verified lab defaults automatically.
Mainak mode mirrors Joey's Miami workflow but swaps the user-specific paths and email to Mainak's setup.
Triton mode requests 16 cores on one host in
normal under brd. Install or set Vina in the unpacked project before submitting docking jobs.Custom mode stores these LSF/HPC values inside the generated package so helper scripts can regenerate matching `.lsf` files later.
Saved!