Reaction Workflows

Graphical workflows for scientific data processing

Reaction Workflows is a graphical environment that enables scientists to build and execute data processing workflows to perform common cheminformatics tasks, such as library enumeration, structure normalization and compound profiling.

What it does

Users build workflows in a drag-and-drop environment by selecting and connecting nodes that provide inputs (e.g a list of reagents) and outputs (e.g. view in Dotmatics Vortex) or perform actions (e.g. perform a reaction), configuring them with data and then executing the workflow to produce results.

Many different tasks can be configured including:

  • Synthetic library enumeration for an ELN experiment
  • Virtual library enumeration and profiling for virtual screening
  • Structure normalization for registration
  • Idea generation via lead hopping or to avoid liabilities
  • Chemistry file clean up


  • Efficient development – graphical programming is faster and more efficient than scripting for cheminformaticians, and produces a self-documented result that's better for reuse and sharing
  • Captures best practice – the workflows allow experts to capture their best practice and then publish to non-experts to configure with their own data and execute
  • No programming skills required – easy-to-use for scientists to produce their own ad-hoc workflows without any knowledge of programming or scripting
  • Immediate productivity – the easy-to-learn graphical environment combined with extensive content already built into the nodes means that users will be up and running very quickly
  • Integrated – seamlessly integrated into the Dotmatics suite
    • Browser hitlists and Chemselector carts become data sources in the reagent node
    • Push and pull to Vortex for analysis and visual selection, 
    • Send a synthetic library reaction scheme directly to Studies Notebook to create an ELN experiment for each step
  • Accessible – the client is web-based for easy deployment, server can be hosted in the cloud or on-premise


Key Features

  • A rich set of data processing nodes to build workflows
    • Cheminformatics action nodes – reaction-based enumeration, chemical transformation, scaffold-based enumeration, structure normalization
    • Calculate/filter nodes – by properties and substructures
    • Visualization nodes – structure grid visualizer, view/select in Vortex, send to Studies Notebook
    • Input/output – SD, smiles, CSV files or interactive molecular drawing
    • Note – document the workflow for sharing
  • Nodes are populated with extensive content (Stores) to allow uses to be productive straightaway
    • 50+ standard literature reactions, 100+ standard transformations, more than 1500 library scaffolds and 60+ normalization rules
    • Common eMolecules reagents lists from Dotmatics ChemSelector
    • Common property profiles such as rule of 3/5 and substructure profiles such as PAINS filters
  • Stores can be augmented with user/group/company data and collections
  • A portal interface provides a simple environment to load data and run published protocols

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