SpaceCompare

Overview

SpaceCompare is a novel tool for comparing and analyzing ultra-large combinatorial chemical spaces. For the first time, users can compare trillion-sized chemical spaces using the combinatorial algorithmic approach of SpaceCompare.

The tool has three modes of operation

overlap calculation of two combinatorial spaces
distribution computation for five well-known physicochemical properties
chemical space optimization by removal of fragments with undesired

Datasets

To use SpaceCompare on an existing chemical space, you can access the Knowledge Space in its topological fragment space representation at https://www.zbh.uni-hamburg.de/forschung/amd/datasets/knowledgespace.html.

Software Availability

SpaceCompare is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download SpaceCompare, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run SpaceCompare. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Bellmann, L.; Penner, P.; Gastreich, M.; Rarey, M. Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. J Chem Inf Model 2022, 62 (3), 553-566. DOI: https://doi.org/10.1021/acs.jcim.1c01378