Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach

摘要

An illustrative example for the effects of related fingerprints on similarity measures. A hypothetical fingerprint scheme with nine bit keys (F1 to F9) is used to represent small molecules in a hypothetical compound dataset. The fingerprint matrix of this dataset is found to have a perfect multicollinearity in the first four features with 2F1=F2+F3+F4. The similarity of a query compound against three compounds is computed using Tanomoto coefficient (Tc) with and without this collinearity. For the results without the collinearity, the Tanimoto coefficient without the first four features (F1 to F4) is shown