Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches.

The success of ligand-based virtual-screening calculations is influenced highly by the nature of target-specific structure-activity relationships. This might pose severe constraints on the ability to recognize diverse structures with similar activity. Accordingly, the performance of similarity-based methods strongly depends on the class of compound that is studied, and approaches of different design and complexity often produce, overall, equally good (or bad) results. However, it is also found that there is often little overlap in the similarity relationships detected by different approaches, which rationalizes the need to develop alternative similarity methods. Among others, these include novel algorithms to navigate high-dimensional chemical spaces, train similarity calculations on specific compound classes, and detect remote similarity relationships.