Interactions Between Weighting Scheme and Similarity Coefficient in Similarity-Based Virtual Screening

Abstract

Similarity searching is one of the most common methods for ligand-based virtual screening, and is normally carried out using the Tanimoto coefficient with binary fingerprints. However, a recent study has suggested that it may be less appropriate for use with weighted fingerprints in some circumstances. This paper compares the Tanimoto coefficient with other coefficients, and demonstrates that one of these, the cosine coefficient, exhibits a much greater degree of robustness in the face of variations in the nature of the fragment weighting scheme that is being used.