Viewer
Upload files to visualize/select conditional information
OMTRA Help Center
01Workflow Modes
🚀 De Novo Design
Generate new chemical structures from scratch.
🧬 Docking
Dock existing ligands into a protein pocket.
02Defining the Pocket
- AReference Ligand
Upload a ligand file (.sdf). The pocket is defined within 8Å of this ligand.
- BDetected Pockets
Upload a protein to auto-detect binding sites using Pocketeer. Select one to define the pocket.
- CManual Coordinates
Manually set X, Y, Z center and box size.
03Sampling
Adding pharmacophore constraints
- Upload a pharmacophore file: Upload an SDF file and select pharmacophore spheres interactively. Alternatively, upload a JSON file with pharmacophore features exported from Pharmit or using this script.
- Select constraints: Pharmacophores appear as wireframe spheres in the 3D viewer. Click any sphere to select it as a conditioning constraint (solid = selected). We recommend selecting fewer than 8.
Fix structure (partial generation)
- By fragment or by atom: For protein-conditioned de novo and rigid docking, open Fix structure on the reference/docking SDF. Use BRICS fragments for quick scaffold locking, or switch to per-atom mode for arbitrary subsets.
- 3D selection: Click to toggle; hold Shift and drag to box-select.
- Results: Fixed atoms are highlighted in amber in the output 3D viewer.
Key Parameters
- Sampling Steps: Number of integration steps. Higher values improve quality (we used 200 in our paper).
- Atom Count Distribution: Sets the distribution of atom counts for generated molecules. Auto-populated when a reference ligand is used to define the pocket.
04Job Output
📊 Metrics Table
Each generated molecule is scored with drug-likeness properties (QED, LogP, molecular weight) and, for protein-conditioned jobs, docking metrics (Vina score, clashes, HB interactions). Click any row to load that molecule in the 3D viewer.
🧪 3D Viewer & Downloads
View generated molecules in 3D alongside the protein and binding pocket. Download individual molecules as SDF files, or view 2D interaction diagrams (PoseView) for protein-conditioned jobs.