Verification of protein structures: patterns of nonbonded atomic interactions

Abstract

A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interactions is described. Different types of atoms are distributed nonrandomly with re-spect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods. Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (0). This leads to six dif-ferent combinations of pairwise noncovalently bonded interactions (CC, CN, CO, NN, NO, and 00). A qua-dratic error function is used to characterize the set of pairwise interactions from nine-residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misreg-istered can then be identified by analysis of the pattern of nonbonded interactions from each window