Chemical Spaces

The Next Generation of Massive Molecule Collections

BioSolveIT pioneers in developing and exploring individual Chemical Spaces: Molecule collections comprising billions and trillions of entries that can be efficiently screened in a reasonable timeframe.
Chemical Spaces are created by combining building blocks with predefined chemical reaction rules. Unlike enumerated molecule libraries, entries are not explicitly listed; instead, combinatorial Chemical Spaces allow a fast and dynamic generation of compounds, enabling rapid processing — delivering only relevant results that are synthetically accessible, or simply purchasable (depending on the Chemical Space).

Combinatorial Marvel

Chemical Spaces surpass the constraints of exhaustively enumerating sets of molecules — yet cover all entries. Rocket Science!
Chemical Spaces consist of two elements: Building blocks on the one hand side, and chemistry rules on how to combine them on the other. When they both come together, a combinatorial explosion occurs, resulting in an astronomical number of compounds. This, in turn, broadens the exploration scope by generating a dataset that encompasses every synthetically accessible possibility.

Our BioSolveIT technology will dive into the molecular zillions and retrieve only those molecule that are relevant to your drug discovery project, without wasting resources on insignificant entries.
Still, a comprehensive evalution of the entire Chemical Space is conducted, ensuring that every potential molecule has the opportunity to be featured as a result.

Chemical Spaces — Commercial Sources for Compounds

Several applications developed by BioSolveIT are available to mine relevant chemistry from the ultra-vast Spaces.
The accessibility of retrieved molecules can be coupled to widely popular on-demand services: Compounds retrieved from one of our various partners' Chemical Spaces can be purchased and delivered to your location within a few weeks typically.

Virtual Chemical Spaces


Let’s compare Chemical Spaces to sauerkraut. The concept of fermented cabbage exists in many world cuisines; kimchi in Korea, kapusta kiszona in Poland, curtido in El Salvador. Although they follow similar preparation steps, the taste varies greatly due to the local ingredients used. Chemical Spaces behave alike: The knowledge and building blocks used to build up the Chemical Space differ between companies and methods involved. The overlaps between two Chemical Spaces can be surprisingly minuscule (Lessel et al. 2019 and Rarey et al. 2021).
By searching in several Chemical Spaces you will maximize your success rate to find diverse, promising molecules.
After performing a search with infiniSee your results will be presented in a table. The column "Source" tells you the origin of the Chemical Space that contains your solution; the ID of the respective result molecule is shown in the "Name" column.
Compounds can be ordered by sending a quote request to the compound vendor with the following information:
Requested structures in SMILES or SD format, Compound ID (concatenated), and amount requested.

For compounds from Ambinter's AMBrosia Space, send your request to
For compounds from eMolecule's eXplore Space, send your request to
For compounds from Enamine's REAL Space, send your request to
For compounds from WuXi's GalaXi Space please send your request to
For compounds from OTAVA's CHEMriya Space please send your request to
For compounds from Chemspace's Freedom Space please send your request to
In this post, we explain the difference between combinatorial, ultra-vast Chemical Spaces and their exhaustive counterpart, enumerated compound libraries.
The building blocks and chemical reactions used in the creation of our partners' Chemical Spaces are not available to the general public.

As for the eXplore Chemical Space, a is available here (PDF). It contains the reactions as SMARTS definitions that were cherry-picked by eMolecules for the creation of the Space.

A helpful collection robust chemistry reactions for computational chemists can be foundfollowing this link.

Sophisticated Software Solutions for Computational Chemists

infiniSee comes with a state-of-the-art graphical user interface that is is easy to operate, enabling effortless navigation for medicinal and computational chemists, as well as other drug hunters, to seamlessly search for compounds and assess the results.
The various Chemical Space search methods (so-called "Components") are also available as command line tools that can be integrated into your consisting workflows. Computational chemists can use advanced setting for large-scale mining of relevant compounds to fine-tune their results.
Those additional settings include:
  • FTrees: expansion of alternative results/alternative synthesis routes
  • SpaceLight: selection of different fingerprints (e.g., ECFP, fCSFP, iCSFP, tCSFP and their respective variants)
  • SpaceMACS: SMARTS definition
  • ... and many more for each tool

Available Command Line Tools for Chemical Space Exploration

Conquer the Chemical Space with BioSolveIT

The fact that the enumeration of compounds has computational limits led to the widespread acceptance within the pharmaceutical industry of utilizing combinatorial Chemical Spaces to harness the potential of in-house building blocks and expertise in chemistry.
The accessibility of results, coupled with intellectual property considerations, further reinforces the adoption of this approach. Expanding the hunting grounds for novel compounds within these Chemical Spaces not only addresses the limitations posed by computational constraints but also opens up new avenues for discovery, allowing pharmaceutical researchers to explore a broader spectrum of potential drug candidates.

Create Your Own Chemical Space
... Or Ask Us to Create One for You

Sometimes the perfect solution is within reach in your own compound library without realization. Design your own, bespoke Chemical Space with your accumulated, in-house knowledge and resources. Reactions and building blocks can be defined to create massive numbers of virtual compounds. Multiple big pharma companies have built their own corporate, in-house Chemical Spaces to search for scaffold alternatives to reduce costs and time.

With years of experience in getting the most out of your resources, BioSolveIT has created dozens of Chemical Spaces. The Spaces generated by our software are recognized as the largest compound sets among pharmaceutical companies.
Considering your in-house proprietary building blocks and chemistry knowledge, we tailor a unique Chemical Space that encompasses the full spectrum of synthesizable potentials as a source for ideation of accessible compounds.