Comparing structural fingerprints using a literature-based similarity benchmark

Extended-connectivity fingerprints of diameter 4 and 6 are among the best performing fingerprints when ranking diverse structures by similarity, as is the topological torsion fingerprint. However, when ranking very close analogues, the atom pair fingerprint outperforms the others tested. When ranking diverse structures or carrying out a virtual screen, we find that the performance of the ECFP fingerprints significantly improves if the bit-vector length is increased from 1024 to 16,384.Graphical abstractAn example series from one of the benchmark datasets. Each fingerprint is assessed on its ability to reproduce a specific series order.