Freedom Space 4.0
The creation and exploration of chemical spaces are essential for early-stage drug discovery because they expand the diversity of compounds available to screen for potential drug candidates. The demand for creating chemical spaces is constantly growing since the development of large databases like Enamine REAL Space.
Here we are introducing Freedom Space – an ultra-large chemical space designed to facilitate your hit discovery workflows by solving the problem of synthetic accessibility. The specialty of this product is the use of Machine Learning (ML) based filters, that were trained on the reaction success data from Enamine. The latest version – Freedom Space 4.0 includes 142 billion molecules, that can be synthesized in 4-5 weeks with a high success rate.
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Options & Access
Freedom Space 4.0 is now available as a synthon-based space with 142 billion molecules, as well as in an the enumerated format. We offer you 2 enumerated subspaces – Rule of Five (Ro5) and Beyond Ro5. Such an approach allows you to choose the most suitable subspace according to the specifics of your project. How to access?
Rule of 5 Space:
- Search compounds from 5B subset from Ro5 space on chem-space.com.
- Download using FTP (access instructions in PDF).
Beyond Rule of 5 Space:
- Download using FTP (access instructions in PDF).
Synthon-based Space:
- Available for similarity search through InfiniSee by BioSolveIT.
- Search compounds using super-structure or similarity search option through Hyperspace developed by Alipheron.
- Available for synthon-based search via the RDKit Library.
Options & Access
Freedom Space 4.0 is now available as a synthon-based space with 142 billion molecules, as well as in an the enumerated format. We offer you 2 enumerated subspaces – Rule of Five (Ro5) and Beyond Ro5. Such an approach allows you to choose the most suitable subspace according to the specifics of your project. How to access?
Rule of 5 Space:
- Search compounds from 5B subset from Ro5 space on chem-space.com.
- Download using FTP (access instructions in PDF).
Beyond Rule of 5 Space:
- Download using FTP (access instructions in PDF).
Synthon-based Space:
- Available for similarity search through InfiniSee by BioSolveIT.
- Search compounds using super-structure or similarity search option through Hyperspace developed by Alipheron.
- Available for synthon-based search via the RDKit Library.
Options & Access
Freedom Space 4.0 is now available as a synthon-based space with 142 billion molecules, as well as in an the enumerated format. We offer you 2 enumerated subspaces – Rule of Five (Ro5) and Beyond Ro5. Such an approach allows you to choose the most suitable subspace according to the specifics of your project. How to access?
Rule of 5 Space:
- Search compounds from 5B subset from Ro5 space on chem-space.com.
- Download using FTP (access instructions in PDF).
Beyond Rule of 5 Space:
- Download using FTP (access instructions in PDF).
Synthon-based Space:
- Available for similarity search through InfiniSee by BioSolveIT.
- Search compounds using super-structure or similarity search option through Hyperspace developed by Alipheron.
- Available for synthon-based search via the RDKit Library.
Space Generation
To create Freedom Space 4.0, we first created a collection of building blocks from reliable suppliers based on their price and lead time. As we are using 40 chemical transformations, custom SMARTS patterns were designed to preselect building block pools for each of the reactions. These pools were further refined using the ML-based filters, which were created to ensure high synthesizability of the space. The resulting building blocks were then used to create synthons, which were further enumerated to form Freedom Space 4.0.
Innovational ML-based filters
To ensure high synthesizability of the space it is important to select suitable building blocks that will perform well in the reactions. Historically this has been done manually through iterations of experiments, though we were able to successfully automate this process using machine learning and synthesis success data obtained from years of operation of REAL Space. We utilize a custom synthon-building block molecule representation during the training process to ensure the model is able to correctly process building blocks that share the same synthons, but contain different functional groups. Each building block pool is filtered by a separate model, which means that over 80 models were used for the space creation.Space Applications
- Virtual screening. Explore vast chemical diversity to identify hits with high success rate.
- Hit expansion. Search for molecules with improved properties using Freedom Space 4.0 and Chemspace’s discovery services.
- Grow fragments. Identify and grow the fragments of interest into the direction of choice.