On the optimal contact potential of proteins

Abstract

We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition for the native structure achieving the lower bound leads to the contact energy matrix that is a scalar multiple of the native contact matrix, i.e., the so-called G o potential. We also derive spectral relations between contact matrix and energy matrix, and approximations related to one-dimensional protein structures. Implications for protein structure prediction are discussed. 2007 Elsevier B.V. All rights reserved.

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