Methods for determining the similarity of protein binding sites are often based on the relative positions of specific atoms in the binding site. These methods can have difficulty in determining if two binding sites are similar when they share ligand binding activity but not sequence identity.  The Surflex PSIM similarity metric compares the protein surfaces presented in binding-site concavities. This methodology is agnostic to the sequence of the protein and focuses on the environment presented to a putative ligand. This ligand-centric view is able to sense both the acute differences between binding sites determined by very similar sequences within a family and the similarities between binding sites with dissimilar sequences which all bind a common ligand. Applications of the method to a variety of protein data sets of differing diversity will be presented.

Surflex PSIM: Ligand-based protein binding site similarity

243rd National Meeting (2012)

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