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Product · Workflows

Built around the questions chemists actually ask.

14 ready-made workflows in 3 problem families. Each one is a tested chain of tools with its file formats and hand-offs already connected: add your inputs, check the estimate, and run.

Browse workflowsOr describe your problem

Family 01 · 5 stages

Virtual screening

Find the compounds in a library most likely to bind your target, then rescore the best hits with a stronger method.

Explore virtual screening
[Virtual screening]Fig. 01
[Selected workflow]Pick another in the legend
simple3 steps

Screen a compound library against a target

SMILES → 3D embed → dock

Convert SMILES to 3D structures, detect pockets, then dock with AutoDock Vina.

You provide
Molecules (SMILES), Protein structure (PDB)
Runs on
CPU
Cost cap
$10.00 default
Open in the builder: Screen a compound library against a target (opens in a new tab)
[Virtual screening · what goes in, what comes out]

  1. Your library

    Imatinib
    Nilotinib
    Dasatinib

  2. Your target

  3. A pose in the pocket

Target
ABL1 kinase domain
Structure
PDB 2HYY · 2.4 Å
Polar contacts
6
Shown: imatinib, nilotinib, and dasatinib as a sample library, and the ABL1 kinase domain with imatinib bound, from its crystal structure. Docking returns a pose like this for every compound, ranked by score. Structure: Cowan-Jacob et al. (2007), Acta Crystallogr D Biol Crystallogr.

Family 02 · 6 stages

Structure prediction to docking

Dock against a protein with no solved structure: predict it from sequence, find its pockets, then dock.

Explore structure prediction to docking
[Structure prediction to docking]Fig. 02
[Selected workflow]Pick another in the legend
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
Open in the builder: Dock into a predicted structure without choosing a box (opens in a new tab)
[Structure prediction to docking · what goes in, what comes out]

  1. Your sequence

  2. Its structure

  3. A pose in the pocket

Sequence
273 residues
Structure
PDB 2HYY · 2.4 Å
Ligand
Imatinib
Shown: the ABL1 kinase domain sequence from PDB 2HYY and that entry's crystal structure. The workflow predicts the structure from the sequence with ESMFold2, finds its pockets, then docks your compounds into them. Structure: Cowan-Jacob et al. (2007), Acta Crystallogr D Biol Crystallogr.

Family 03 · 6 stages

Library design

Generate or enumerate new compounds for a target or an SAR series, then dock them.

Explore library design
[Library design]Fig. 03
[Selected workflow]Pick another in the legend
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
Open in the builder: Dock analogs enumerated from your SAR data (opens in a new tab)
[Library design · what goes in, what comes out]

  1. Your series

    Imatinib
    Nilotinib
    Radotinib

  2. A combination not in it

    Radotinib head · Imatinib tail

  3. A pose in the pocket

Series
3 ABL inhibitors
Shared core
Phenylaminopyrimidine
New combination
C28H30N8O
Shown: imatinib, nilotinib, and radotinib, which share a core (highlighted). Free Wilson analysis splits a series into that core and its substituents and enumerates the combinations not yet made, like radotinib's head on imatinib's tail; the workflow then docks them. The pose is imatinib's crystal pose. Structure: Cowan-Jacob et al. (2007), Acta Crystallogr D Biol Crystallogr.

Under the hood

Change any step, or build your own.

Every template opens in the visual builder. The same building blocks are available for your own workflows, and the builder checks each connection as you make it.

[workflow builder]Fig. 04
The workflow builder: a palette of tools on the left; in the middle, the steps Molecule Conversion, Binding-Site Detector, and AutoDock Vina connected to the ligand and target inputs; on the right, the AutoDock Vina step's resource, mode, and payload settings.
“Screen a compound library against a target” open in the builder: tools on the left, steps wired by their typed ports in the middle, and the docking step's hardware, mode, and settings on the right. Screenshot of the app.

Bindings

Each step input is bound to one source:

BindingConnects to
$paramA workflow input you fill in at launch: a file, a list, or a setting.
$fromAnother step's output port, e.g. the poses from a docking step.
$artifactA file already in your library, such as a result from an earlier run.
$constA fixed value written into the workflow.

Typed ports

Every port carries a data kind, so a step only accepts what it can use. Known format conversions, such as SMILES to 3D SDF or CIF to PDB, run between steps automatically.

  • Archive
  • Docked poses
  • Force-field system
  • Kinetic mechanism
  • Molecules
  • Protein sequences
  • Protein structure
  • Sequences
  • Structures
  • Table
  • Trained model

Filters and fan-out

Filter steps reshape results between jobs: deduplicate, filter rows, limit, merge, partition, sample, select top k, split, zip join. A step can also run once per item (scatter): one job per ligand, for example.

Up to 64 steps

Workflows can grow to 64 steps. Each run is estimated before it starts and pauses at its cost cap rather than overspend; you can resume it.

Versions

Saved workflows keep their version history, so you can look back at an earlier version or restore it.

Share and fork

Share a workflow with a link; colleagues fork their own copy to change and run. Export any workflow as JSON.