MAPPIS is a novel method for multiple structural alignment of PPIs which allows recognition of a set of common physico-chemical properties and their interactions without the need to assume similarity of sequential patterns or backbone patterns. We show its application to several biological examples, such as alignment of interfaces of G proteins with their effectors and regulators, as well as previously created clusters of interfaces.
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Shulman-Peleg A, Shatsky M, Nussinov R. and Wolfson H.J.
MultiBind and MAPPIS: Web servers for multiple alignment of protein 3D binding sites and their interactions,
Nucleic Acids Research, 2008, Vol. 36, W260-W264.