Solutions · 4 workflows
Library design
Generate or enumerate new compounds for a target or an SAR series, then dock them.
- Dock analogs enumerated from your SAR dataFree Wilson → 3D embed → dock
- Grow analogs from your SAR table with matched pairs, then dockMatched pairs → analogs → dock
- Generate and dock new ligands for a pocketDrugFlow generate → dock
- Build a library from building blocks, filter it, then dockReaction enumerate → filter → diversity pick → dock
- Workflows
- 4
- Stages
- 6
- Tools
- 10
Your series
Imatinib Nilotinib Radotinib A combination not in it
Radotinib head · Imatinib tail A pose in the pocket
- Series
- 3 ABL inhibitors
- Shared core
- Phenylaminopyrimidine
- New combination
- C28H30N8O
Workflows
Pick the one that fits.
Open any of them in the builder: signed out you get a read-only preview, signed in you can add your inputs, see the estimate for your plan, and run. The cost cap is the default; you can change it at launch, and a run pauses instead of spending past it.
- moderate4 steps
Dock analogs enumerated from your SAR data
Free Wilson → 3D embed → dock
Enumerate analogs with Free Wilson, embed to 3D, detect pockets, then dock with AutoDock Vina.
- You provide
- Molecules (SMILES), Protein structure (PDB)
- Runs on
- CPU
- Cost cap
- $15.00 default
- moderate6 steps
Grow analogs from your SAR table with matched pairs, then dock
Matched pairs → analogs → dock
Apply matched molecular pair transforms mined from your SAR table to make analogs, embed them to 3D, detect pockets, then dock with AutoDock Vina.
- You provide
- Table (CSV), Protein structure (PDB)
- Runs on
- CPU
- Cost cap
- $25.00 default
- moderate4 steps
Generate and dock new ligands for a pocket
DrugFlow generate → dock
Detect a pocket and reference ligand, generate with DrugFlow, cap the set, then dock with AutoDock Vina.
- You provide
- Protein structure (PDB)
- Runs on
- CPU · T4 GPU
- Cost cap
- $25.00 default
- advanced9 steps
Build a library from building blocks, filter it, then dock
Reaction enumerate → filter → diversity pick → dock
Enumerate products from reactant lists and a reaction SMARTS, standardize them, filter for drug-likeness, pick a diverse subset, then dock with AutoDock Vina.
- You provide
- Molecules (SMILES), Reaction smarts, Protein structure (PDB)
- Runs on
- CPU
- Cost cap
- $50.00 default
Related tools
Run any step on its own.
The tools behind these workflows also run individually.
- Free Wilson Analysis
Quantify R-group SAR contributions and predict unsynthesized molecules from activity data
- Molecule Conversion
Convert molecule file/data format
- Binding-Site Detector
Find ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflows
- AutoDock Vina
High performance molecular docking and virtual screening for drug discovery
- Matched Molecular Pairs
Hussain–Rea matched pairs: chemical transforms and activity deltas from a SMILES library
- DrugFlow
Generate candidate ligands from a protein target and reference ligand using flow matching
- Reaction Enumeration
Enumerate product libraries from reaction SMARTS or RXN files and reactant SMILES lists
- Molecule Standardizer
Salt-strip, neutralize, tautomer, and stereo cleanup to parent structures
- Drug-likeness & Structural Alerts
Score and filter molecules with Lipinski, Veber, QED, SA score, and PAINS/Brenk/NIH alerts
- Fingerprint Similarity & Clustering
Tanimoto nearest neighbors, Butina clustering, MaxMin diversity, and Scanpy PCA/UMAP/Leiden clustering from molecular fingerprints