Solutions · 7 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
- Propose R-group combinations with Free-Wilson, then pick the next batch to makeFree-Wilson proposals → pick the next batch to make
- Pick the next compounds to make from your measurements, then dock themPick the next batch from your measurements → dock it
- 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
- Dock the analogs your own model scores bestReaction enumerate → score with your model → dock the best
- Workflows
- 7
- Stages
- 6
- Tools
- 12
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
- simple2 steps
Propose R-group combinations with Free-Wilson, then pick the next batch to make
Free-Wilson proposals → pick the next batch to make
Fit an additive Free-Wilson model to your measured series and enumerate the R-group combinations you have not made, then fit a Gaussian process on the same measurements and pick a batch of those proposals by upper confidence bound with Kriging-believer batches.
- You provide
- Molecules (SMILES)
- Runs on
- CPU
- Cost cap
- $10.00 default
- moderate5 steps
Pick the next compounds to make from your measurements, then dock them
Pick the next batch from your measurements → dock it
Fit a Gaussian process on your measured compounds, pick a batch from your candidate list by upper confidence bound with Kriging-believer batches, embed the picks to 3D, detect pockets, then dock them with AutoDock Vina as a structural check.
- You provide
- Table (CSV), Molecules (SMILES), 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
- advanced9 steps
Dock the analogs your own model scores best
Reaction enumerate → score with your model → dock the best
Enumerate products from a reaction, standardize them, predict a property with one of your saved models, keep the 96 highest, then embed to 3D and dock with AutoDock Vina.
- You provide
- Model id, 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 molecules between SMILES, InChI, SELFIES, MOL/SDF, PDB, and other formats, optionally in 3D
- 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
- Active Learning
Pick the next batch of compounds to make from your measurements, balancing predicted value, uncertainty and diversity
- 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 neighbors, Butina and Leiden clustering, MaxMin diversity picks, and UMAP maps from fingerprints
- MPNN Models
Fast structure-property inference that highlights key molecule substructures