Organic Synthesis Software

Organic Synthesis Software

Reduce the time between chemical target conception and laboratory execution with our new platform for virtual synthesis. The software allows you to filter millions of data points to suit your preferences and find optimized routes to your toughest queries in medicinal chemistry and drug discovery.

This “chemical thinking” software relies on a knowledge base of tens of thousands of expert-defined rules of chemical reactivity, combined with proprietary algorithms to scrutinize millions of synthetic pathways and choose the routes that lead to desired targets in the most cost-effective way.


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   Software and Service Offering



 What is Retrosynthesis?

Retrosynthetic analysis or retrosynthesis is an intellectually intensive process by which organic syntheses are planned. Chemists rely on their knowledge that good databases to look at precursor structures of a target molecule in order to find simpler and simpler structures and map the synthetic route back to commercially available starting materials.

The retrosynthesis module in our organic synthesis software makes it possible to quickly navigate back and forth through synthetic possibilities as though evaluating chess moves with a virtual assistant. Let the software keep track of chemical context and design a synthetic pathway for known or unknown target molecules in times ranging from seconds to hours, depending upon the complexity.

Built on:

  • Reactions
  • Reaction classes
  • Conditional rules

Accounts for:

  • Indirect chemical environment
  • Substrate groups needing protection
  • Group incompatibilities
  • Stereo-and regio-chemistry

Easily filter out overly complex synthetic trees, flag cross-reactivity conflicts, and specify other custom preferences while predicting theoretical yields.


 Synthesis Optimization & Planning

We brought network theory together with organic chemistry to build the network module that searches for novel synthetic pathways among 10 million known chemical substances interlinked with as many reactions.

Customize your search to:

  • include a specific intermediate,
  • avoid a toxic substrate,
  • use water soluble substances,
  • hit a particular cost point, and even
  • take advantage of the most readily available chemicals.

 How Does it Work?

The retrosynthesis pathway search strategizes, scoring current and future synthetic moves using the concept of synthetic position. It considers the structural and chemical complexity of the sets of synthons generated in each move and generates a score based on the scores of individual moves, the number of moves, and their synthetic complexity.

Proprietary atom-matching algorithm rules take into account reaction stereochemistry, regiochemistry, and steric and electronic effects. These algorithms also overcome software challenges related to ordering neighboring bonds and bond creation or breakage in the retron versus the synthon.

Our retrosynthesis knowledge base comprises more than 50,000+ reaction rules coded by expert organic chemists as well as auxiliary databases with some 200,000 specialized reactions along with conditional chemical rules, literature references, reaction conditions, and more, all available for user review. Reaction rules are input in the SMILES/SMART format, lending them to quicker large-scale computational processing. This full knowledge of aromatic substitution rules and ability to calculate electron delocalization energies puts both chemical and advanced quantum mechanics modeling at your fingertips.


 How Does it Search?

Apply one or multiple constraints globally, and the software automatically takes a “greedy search” approach, evaluating individual steps before presenting the optimized synthetic pathways. It’s also possible to optimize an entire portfolio to share common substrates and intermediates. In one test case, a small company used our software to trim its production cost on 51 products by more than 45% (See “Parallel Optimization of Synthetic Pathways within the Network of Organic Chemistry).

The software supports globally optimized synthesis of up to 100 steps. Once a search is run, users can easily inspect node sizing to evaluate synthetic feasibility without looking at the chemical structures. The trend of molecular weight against synthetic progress helps determine whether a synthetic pathway is starting from smaller or more popular molecules and progressing toward larger or rarer ones.



 What Others Are Saying

"...taught to learn new rules, as well as to restructure existing knowledge, the software might even throw up ways to make totally new compounds with useful applications.” — New Scientist

"The benefits that can be realized through the use of machine assistance need not be limited to a few specific opportunities, but rather a broader view across all synthesis environments is necessary."— ACS Central Science

"...algorithms to search for pathways quickly, and in a fraction of the time it would take to sift through a database or list."— Chemistry World


 Software and Services Offering

In 2018, customers will be able to choose one of two packages:

  • Now Available! Service: A mix of consulting- and expert-level software execution allows you to provide a target of interest and receive a fully customized route based on your synthetic style and particular needs. Consult one on one with our experienced organic chemists to receive viable synthetic pathways for your novel chemical targets under a confidential disclosure agreement (CDA). Skip the learning curve of a new software and contact us to receive your hand-picked reaction pathways today.
  • License: Allows for access to the software, training, and additional support during a defined period.

Contact us to request Information or a quote.

Our organic synthesis software is only available under limited release at this time.