RISC and Dense Fingerprints
A more in-depth analysis of RISC shows that its reported performance for 1024- and 2048-bit fingerprints does not extend to many other fingerprint types of the same size. While faster than chemfp’s BitBound for the atypically sparse Morgan circular fingerprints, its performance is comparable to BitBound for other types with similar density, and significantly slower as bit densities increase above around 0.1. This analysis uses 23 different combinations of fingerprint types and sizes from RDKit, OpenEye, and Open Babel. The fingerprints were generated using randomly selected structures from ChEMBL 24.