Solutions · 4 workflows
Structure prediction to docking
Dock against a protein with no solved structure: predict it from sequence, find its pockets, then dock.
- Dock into a predicted structure without choosing a boxSequence → fold → DiffDock
- Dock against a protein with no solved structureSequence → fold → dock
- Dock into a cleaned predicted structure and see the contactsSequence → fold → prepare → dock → PLIP
- Compare docking against a wild type and its point mutantsPoint mutants vs wild type → fold → dock → compare
- Workflows
- 4
- Stages
- 6
- Tools
- 8
Your sequence
Its structure
A pose in the pocket
- Sequence
- 273 residues
- Structure
- PDB 2HYY · 2.4 Å
- Ligand
- Imatinib
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.
- simple3 steps
Dock into a predicted structure without choosing a box
Sequence → fold → DiffDock
Fold a protein sequence with ESMFold2, dock a SMILES library blind with DiffDock, and keep the top-confidence poses.
- You provide
- Molecules (SMILES), Protein sequence
- Runs on
- A10 GPU · T4 GPU
- Cost cap
- $110.00 default
- moderate4 steps
Dock against a protein with no solved structure
Sequence → fold → dock
Fold a protein sequence with ESMFold2, detect pockets, embed ligands to 3D, then dock with AutoDock Vina.
- You provide
- Molecules (SMILES), Protein sequence
- Runs on
- CPU · A10 GPU
- Cost cap
- $25.00 default
- advanced7 steps
Dock into a cleaned predicted structure and see the contacts
Sequence → fold → prepare → dock → PLIP
Fold a sequence with ESMFold2, repair and protonate the model, detect pockets, dock with AutoDock Vina, then profile the top poses' interactions with PLIP.
- You provide
- Molecules (SMILES), Protein sequence
- Runs on
- CPU · A10 GPU
- Cost cap
- $25.00 default
- advanced10 steps
Compare docking against a wild type and its point mutants
Point mutants vs wild type → fold → dock → compare
Apply up to 10 point mutations to a protein sequence (each checked against the wild-type residue), fold the wild type and every mutant with ESMFold2, dock the same ligands into each structure's top pocket with AutoDock Vina, then compare every mutant's affinity for each ligand with the wild type's.
- You provide
- Molecules (SMILES), Sequence
- Runs on
- CPU · A10 GPU
- Cost cap
- $100.00 default
Related tools
Run any step on its own.
The tools behind these workflows also run individually.
- ESMFold2
Predict protein, DNA, RNA, and ligand complex structures with evolutionary scale modeling
- DiffDock
Protein-ligand docking with diffusion models and confidence-ranked poses
- 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
- Protein Preparer
PDBFixer cleanup, PDB2PQR protonation, and dock-ready structures without MD solvation
- Interaction Profiler
Enumerate hydrogen bonds, hydrophobics, salt bridges, and π-stacking in docked complexes
- Sequence Mutator
Apply point mutations such as T315I to a protein sequence, checking each wild-type residue