SpaceLight is a novel search method for similarity-driven virtual screening in large combinatorial fragment spaces using topological fingerprints. It utilizes the well-known ECFP and the Connected Subgraph Fingerprint (CSFP) to describe molecular similarity. In contrast to existing workflows using fingerprint methods, the SpaceLight approach is able to exploit the combinatorial character of fragment spaces and consequently can conduct similarity searches considering billions of compounds within seconds on a standard PC. In addition fragments forming scaffolds can be retreived to identify reaction routes for compounds and custom fragment spaces can be generated.
The SpaceLight tool is available for Linux, MacOS, and Windows as part of the NAOMI ChemBio Suite at https://uhh.de/naomi and is free for academic use and evaluation purposes.
To search with SpaceLight you can access the Knowledge Space in its topological fragment space representation at https://www.zbh.uni-hamburg.de/forschung/amd/datasets.html#knowledge