All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

Figure 1

HIV-1 protease (a) ribbon and (b) atomic ball-and-stick diagrams. The atomic coordinates are used as tetrahedral vertices to generate (c) the Delaunay tessellation of the protein chain, a convex hull consisting of thousands of space-filling and nonoverlapping tetrahedra, each of whose vertices objectively identifies a quadruplet of nearest neighbor atoms. The modified tessellation in (d) is obtained by removing all edges longer than 12 Å between pairs of atoms, thereby eliminating all tetrahedra that share those edges and excluding their corresponding atomic quadruplets from consideration as nearest neighbors.