Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains

Article Abstract:

The study employs the umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation to calculate and parameterize the potentials of mean force of identical hydrophobic side chains of amino acid. The analysis of the positions and depths of the contact minima and the positions and heights of the desolvation maxima proves and confirms the application of such potentials in coarse-grain protein-folding simulations.

Analysis, Protein folding, Amino acids, Structure, Hydrophobic effect

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Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization

Article Abstract:

The application of hierarchical optimization of protein potential-energy landscapes to optimize the UNRES force field using multiple training proteins is reported. The resulting force field trained on a set of four proteins gives good medium-resolution predictions of the structures of most of the alpha- and the alpha + beta-proteins, but still could not handle nontrivial beta-motifs sufficiently well.

Proteins, Potential energy

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