Profile scaling increases the similarity search performance of molecular fingerprints containing numerical descriptors and structural keys

The concept of compound class-specific profiling and scaling of molecular fingerprints for similarity searching is discussed and applied to newly designed fingerprint representations. The approach is based on the analysis of characteristic patterns of bits in keyed fingerprints that are set on in compounds having equivalent biological activity. Once a fingerprint profile is generated for a particular activity class, scaling factors that are weighted according to observed bit frequencies are applied to signature bit positions when searching for similar compounds. In systematic similarity search calculations over 23 diverse activity classes, profile scaling consistently increased the performance of fingerprints containing property descriptors and/or structural keys. A significant improvement of similar to15% was observed for a new fingerprint consisting of binary encoded molecular property descriptors and structural keys. Under scaling conditions, this fingerprint, termed MP-MFP, correctly recognized on average close to 60% of all active test compounds, with only a few false positives. MP-MFP outperformed MACCS keys and other reference fingerprints. In general, optimum performance in scaling calculations was achieved at higher threshold values of the Tanimoto coefficient than in nonscaled calculations, thereby increasing the search selectivity. In general, putting relatively high weight on signature bit positions that were always, or almost always, set on was found to be the most effective scaling procedure. Analysis of class-specific search performance revealed that profile scaling of MP-MFP improved the similarity search results for each of the 23 activity classes.