The SPPIDER protein interface recognition server can be used to: (1) predict residues to be at the putative protein interface(s) by considering single protein chain with resolved 3D structure; (2) analyse protein-protein complex with given 3D structural information and identify residues that are being in interchain contact.
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Proteins. 2007 Feb 15;66(3):630-45.
Prediction-based fingerprints of protein-protein interactions.
Porollo A1, Meller J.