Abstract
One of the approaches to protein structure prediction is to obtain energy functions which can recognize the native conformation of a given sequence among a zoo of conformations. The discriminations can be done by assigning the lowest energy to the native conformation, with the guarantee that the native is in the zoo. Well-adjusted functions, then, can be used in the search for other (near-) natives. Here the aim is the discrimination at relatively high resolution (RMSD difference between the native and the closest nonnative is around 1 A) by pairwise energy potentials. The results show that the potential can be trained to discriminate between the native conformation of one protein as the (near-) global minimum, and other nonnatives, including energy-minimized ones (or local minima). This potential function is able to identify the native conformation of another protein, too.
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