Identifying surface binding pockets.

<p>(<b>A</b>) Bcl-X_L (<i>grey surface</i>) is shown in complex with an inhibitor (<i>blue sticks</i>). The protein surface features a large pocket (<i>red spheres</i>) complementary in shape to the inhibitor. (<b>B</b>) Deep pocket volumes of surface pockets at protein interaction sites harboring a bound inhibitor (<i>red line</i>) are larger than those found elsewhere on the protein surface (<i>black line</i>). Data are collected from a test set of seven proteins, each of which has been solved in complex with a small-molecule inhibitor (Bcl-X_L, IL-2, FKBP12, HPV E2, ZipA, MDM2, and the BIR3 domain of XIAP).