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ZBH
ZBHCenter for Bioinformatics

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SpaceLight & SpaceLightN

Overview

SpaceLight is a search method for similarity-driven virtual screening in large combinatorial fragment spaces with topological fingerprints. It utilizes the well-known ECFP and the Connected Subgraph Fingerprint (CSFP) to describe molecular similarity. In contrast to existing workflows based on fingerprint methods, the SpaceLight approach exploits the combinatorial nature of fragment spaces. Consequently, it can conduct similarity searches considering billions of compounds within seconds on a standard computer. Furthermore, users can retrieve scaffold-forming fragments to identify reaction routes for compounds. Using this feature, they can generate custom fragment spaces.

Please note that with SpaceLight, you can build and search your own spaces. It is only compatible with the KnowledgeSpace and the SAVI-Space.

SpaceLightN, which is based on SpaceLight as distributed by BioSolveIT, also supports weighted fingerprint searches. However, its applicability is currently restricted to the SAVI-Space.

Datasets

To search with SpaceLight, you can access the KnowledgeSpace in its topological fragment space representation at https://www.zbh.uni-hamburg.de/forschung/amd/datasets/knowledgespace.html. You can also read and use the SAVI-Space at https://www.zbh.uni-hamburg.de/en/forschung/amd/datasets/savi-space.html for SpaceLight searches.

Software Availability

SpaceLight and SpaceLightN are freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download SpaceLight or SpaceLightN, 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 SpaceLight and SpaceLightN. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Bellmann, L.; Penner, P.; Rarey, M. Topological Similarity Search in Large Combinatorial Fragment Spaces. J Chem Inf Model 2021, 61 (1), 238-251. DOI: https://doi.org/10.1021/acs.jcim.0c00850

Lübbers, J.; Schokolowski, M.; Lessel, U.; Weber, A.; Rarey, M. Guiding Similarity Search in Chemical Fragment Spaces with Weighted Fingerprints. J Chem Inf Model 2026, 66 (4), 2220-2229. DOI: https://doi.org/10.1021/acs.jcim.5c02952