Molecular shape is a useful tool for identifying small-molecules for therapeutics. Shape similarity can be found through both alignment methods, a computationally demanding approach, or through feature vector methods, computationally less demanding. Maximization of both volume overlap and various feature points makes alignment methods computationally intensive. The computational burden of alignment can be reduced by pre-aligning shapes. Our recently published Volumetric-Aligned Molecular Shapes (VAMS) search pre-aligns the entire molecule, and was shown to be effective as a pre-screen. The introduced method, fragment oriented molecular shape (FOMS) search, pre-aligns shapes to only a part of the shape (e.g. a deeply buried fragment). This eliminates the burden of aligning shapes, so large libraries consisting of millions of shapes are searched on the scale of a few seconds, at the loss of accuracy. FOMS outperforms VAMS for simple protein-ligand interactions. FOMS’ performance for complex protein-ligand interactions is also explored.

Fragment oriented molecular shape (FOMS) search: A novel shape-based virtual screening method

251st National Meeting (2016)

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