There are many existing methods for molecular alignment, taking a variety of different approaches to the problem of aligning molecules to assess similarity and differences in their shared shapes and chemical features. A major problem in the evaluation and validation of these methods has been the lack of a gold standard alignment methodology to which the results from other approaches can be compared. Here we present an exhaustive molecular alignment method we term subROCS. The alignments from subROCS are compared to a set of alternative methods using rigorous statistical comparisons. The impact of superior alignments in scoring and ranking molecules versus a reference, where better alignments are expected to provide better performance in lead discovery, is also explored.

Exhaustive pairwise overlays: the gold standard for molecular alignment?

249th National Meeting (2015)

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