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Updated: Aug 3, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 16, 2010
Simplified calculation of folding energies and residue coordination numbers in random heteropolymers
1Department of Physics, CB 1105, Washington University, St. Louis, Missouri 63130, USA.
Abstract:
I develop a formalism for calculating effective pair and higher-order interactions between residues in random heteropolymers that approximately predict the folding enthalpy and the coordination numbers of individual residues. In a simple model heteropolymer with additive couplings between residues, the folding enthalpy is written in terms of two-, three-, and four-body interactions between residues. The coordination numbers are expressed in terms of interactions between up to three residues. Application to a 6x6 square model shows that the folding enthalpy is obtained to an accuracy of better than 1%. The coordination numbers are obtained with a rms error of 1.2 neighbors.
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