SpaceLight

Overview

SpaceLight is a novel 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.

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.

Software Availability

SpaceLight is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download SpaceLight, 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. 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