Protein surface roughness and small molecular binding sites.

Pharmaceutical design is usually directed at developing small molecules that can specifically bind and alter the activity of a target protein. Here, we show that high-affinity binding of small molecules requires a rough patch on a protein surface. Drug design strategies should therefore be targeted to rough areas on a protein. Our results indicate that the roughness of small functional sites may reflect the complex local shapes needed to fit specific interactions into small areas. Copyright 1999 Academic Press.