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

Figure 2

Graphical representations for two four-body potentials, based on an eight-letter alphabet with a 12 Å edge-length cutoff, and a twenty-letter alphabet with a 4.8 Å edge-length cutoff. Here = alpha-carbon, = backbone carbonyl-carbon, and = side-chain sulfur (from either cysteine or methionine) represent the same atom types in both alphabets, with quadruplets and appearing at the same extremes of both potentials. Despite millions of tetrahedra generated by the 1417 protein tessellations irrespective of the cutoff length (see Table 1), note that 3 of 330 atomic quadruplet types (, and ) did not appear at all as tetrahedral vertices based on an 8-letter atomic alphabet with a 12 Å cutoff ( = side-chain nitrogen atom), while 1935 of 8855 quadruplets types were not observed under a 20-letter alphabet with a 4.8 Å cutoff.

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