WHISCY (What information does surface conservation yield?) is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.
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De Vries SJ, van Dijk ADJ, and Bonvin AMJJ
WHISCY: What information does surface conservation yield? Application to data-driven docking.
Proteins: Struc. Funct. & Bioinformatics; 2006, 63(3): 479-489.