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Chemaxon Structure Enumeration Toolkit

Top of the line chemical reaction enumeration and Markush enumeration

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Structure Enumeration Toolkit

The success of drug discovery relies heavily on how deeply you explore the chemical space around your leads.

The Structure Enumeration Toolkit allows you to enumerate virtual libraries and generate molecule fingerprints. This helps you fully explore the chemical space around your leads and make the best possible decisions grounded in science.

Structure Enumeration Tools

Reactor

Reactor is a high-performance reaction enumeration engine that applies defined reaction schemas to large reactant sets to generate chemically feasible, synthesizable product libraries.

  • Chemically feasible virtual reactions at scale using user-defined reaction schemas
  • Supports reaction-definition in SMIRKS/SMARTS, RDF, RXN, MRV, etc.
  • Built-in and growing library of organic reactions
  • Full manual control for focused library design
  • “Chemical Terms” rule engine enforce reaction intelligence
  • Stereochemistry-aware enumeration
  • Flexible library generation modes

Markush Enumeration

Markush or generic structures are widely used in combinatorial libraries and chemical patents to define large chemical spaces. Highlighted Markush features our technology can handle:

  • Atom and bond lists
  • Position variation bonds
  • Link nodes
  • Repetition units
  • Multiply connected R-groups
  • Heavily nested R-groups
  • R-group bridges
  • Homology groups and enumeration
  • Full, partial and random Markush enumeration
  • Library size calculation

Availability

The Toolkit bundles are built to easily integrate with most systems using a range of different APIs including Java, Python, Microservices and .NET.

Toolkit Offerings

Tools Discovery Toolkite Descriptor Generation Toolkit Structure Preparation Toolkit Structure Enumeration Toolkit Naming Toolkit
hERG Inhibition

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Elemental Analysis

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Partitioning

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Solubility

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NMR Predictor

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Structural Calculations

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Isomers

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Protonation

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Standardizer

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Structure Checker

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Reactor

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Markush Enumeration

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Chemical name and structure conversion

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Workflow-Specific Toolkits

Our workflow-specific offerings are designed to serve your needs with a targeted subset of tools bundled together.

Discovery Toolkit

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Descriptor Generation Toolkit

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Structure Preparation Toolkit

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Naming Toolkit

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With Discovery Toolkit, your data is secure

Certara holds ISO 27001 certification for Certara’s Information Security Management System (ISMS). We have implemented robust security controls, undergone rigorous risk assessments, and continuously strive for improvement. Discovery Toolkit ensures full compliance with global data protection standards, offering peace of mind for sensitive analysis.

Learn more in our Trust Center

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Why Certara

Certara delivers leading-edge solutions that empower scientists to make data-driven decisions, accelerating drug discovery timelines and improving outcomes.

Early drug discovery is a core area of expertise at Certara, supported by a team of highly experienced and renowned experts in the field.
The dynamic community of users from drug discovery empowers us to continuously refine our solutions to meet the ever-evolving demands of innovative research.

Using Chemaxon’s suite of tools as core components of our chemistry workflows, they save us time while supporting strong, science-driven decisions. What sets them apart is that their team is professional, approachable, and genuinely invested in helping us succeed.

Xin Zhang
Sr. Director, Cheminformatics and AI/ML
Cellarity

Book a Demo

Discovery Toolkit contains every cheminformatics toolkit we have to offer.

For more specific needs, we offer workflow-specific bundles:

Descriptor Generation Toolkit
Structure Preparation Toolkit
Structure Enumeration Toolkit
Naming Toolkit

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