FINDSITE is a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.
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Skolnick J and Brylinski M (2009)
FINDSITE: a combined evolution/structure-based approach to protein function prediction.
Brief Bioinform 10:378-91