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The prediction of functional sites including ligand binding sites or catalytic sites can guide the design of small molecules that could interact with a protein and modulate its function or drive the selection of targeted mutations for protein engineering. It largely relies on the identification and characterization of clefts and cavities in protein structures.
(Schmidtke et al., 2010) fpocket: online tools for protein ensemble pocket detection and tracking. Nucleic Acids Res.