SpaceLightN

SpaceLightN is a command line tool from Prof. Rarey (University of Hamburg) for similarity-based virtual screening in large combinatorial fragment spaces. It utilizes well-known fingerprints methods such as the Extended Connectivity Fingerprints (ECFP) and is able to search spaces containing billions or even trillions of compounds within seconds on a standard PC.

More details here https://www.zbh.uni-hamburg.de/forschung/amd/software/spacelight.html

The NAOMI ChemBio Suite 25 contains many other tools https://software.zbh.uni-hamburg.de/documents/NAOMI_ChemBioSuite_09-25.pdf