Motif Matcher: Substructure Search in Vast Chemical Spaces

infiniSee's Motif Matcher dives into extremely vast Chemical Spaces and retrieves compounds containing the specific motif you are seeking within seconds (and sometimes even quicker)!
Advance your substructure-driven campaigns and fragment-based projects to the next level by gaining access to EVERY accessible compound of interest.

Mine for Most Relevant Compounds

From time to time, different drug discovery scenarios can converge to the same outcome: A particular substructure emerges as the leading motif for the upcoming steps.
In such a case, gaining access to a wide array of synthesizable or purchasable compounds that feature that desired scaffold broadens the range of tools available to medicinal chemists. Additionally, this accessibility also accelerates the advancement of the campaign.

The Motif Matcher Mode was developed to address this need: From a huge Chemical Space, It pulls out a user-defined number of compounds that contain your wanted molecular motif. If that motif is not fully there, it will list the next-best compounds. Running the SpaceMACS algorithm, you are able to retrieve up to millions of relevant compounds from combinatorial Chemical Spaces — and the resulting molecules are synthesizable or even purchasable: Collaborations with our premium compound vendor partners opens the door to swiftly acquire your make-on-demand results.

Substructure Search:
Deceptively Simple — Yet Full of Potential

Access to all possible and tangible compounds bearing a particular substructure benefits several application scenarios in modern drug discovery:
  • Fragment-based drug discovery campaigns can mine relevant chemistry with the motif of a confirmed binder to efficiently select candidates for a follow-up.
  • Typically, a QSAR analysis suggests a pharmacophore, which can then serve as a substructure to identify potential candidates to further investigate the pharmacological effects of decorated analogs.
  • Machine learning and AI methods rely on relevant input. SpaceMACS and Motif Matcher retrieve compounds that are synthetically accessible and are therefore valuable sources for the creation of data sets.
  • Sometimes we can't see the forest for the trees. As a medicinal chemist you might be surprised about the kind of results that may be retrieved as your next lead structure when searching in trillions of compounds or beyond.

The combination of access to the largest reservoirs of compounds and computational post-processing (e.g., docking, ligand-based methods, machine learning, you name it) can therefore significantly amplify the success rate of different research projects.

Available as Command Line Tool

The Motif Matcher is available as a command-line tool (SpaceMACS) following this link. Integrate this seamlessly into your existing workflows.
Multiple parameters offer complete command over the compound mining procedure, allowing you to generate datasets of your preferred sizes. Conveniently request results for a list of compounds, generating multiple classically enumerated molecule libraries in a single run.

Original SpaceMACS Publication

Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces.
Schmidt, R.; Klein, R.; Rarey, M.
Journal of Chemical Information and Modeling 2021, 62 (9), 2133-2150.

Abundant Chemical Spaces for Most Effective Solutions

In collaboration with our compound suppliers, several make-on-demand Chemical Spaces have been conceived. Accessing various sources provides your entry to distinct in-house knowledge and exclusive building blocks, leading to the generation of diverse sets of molecules.
Compounds from these Chemical Spaces can be ordered and delivered to your table within a few weeks:
  • REAL Space by Enamine, featuring 44 billion compounds
  • Freedom Space by ChemSpace, featuring 5.1 billion compounds
  • GalaXi by Wuxi LabNetwork, featuring 12 billion compounds
  • eXplore by eMolecules, featuring 7 trillion compounds
  • CHEMriya by OTAVA featuring 12 billion compounds
And, shouldn't you have seen the publication: These spaces have essentially no overlap.

Stay tuned for future news!
If you are interested to test SpaceMACS in early access, please contact us.

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