Evaluation of a mean field potential for protein folding with different interaction centers

María Larriva, David de Sancho and Antonio Rey

Physica A: Statistical Mechanics and its Applications, 2006, vol. 371, issue 2, 449-462

Abstract: We use Monte Carlo simulations to analyze the behavior of a family of previously reported, statistically derived, mean field potentials for protein folding (the DFIRE potentials from the Zhou laboratory). The potentials may consider different interaction centers (alpha carbons, beta carbons, or side-chain centroids), depending on the details of the coarse-grained model simulated. The type of association of the helices in different simulated coiled-coil proteins provides interesting information on the real capabilities of these interaction schemes along the sampling of the topological space available to the protein model.

Keywords: Protein folding; Mean field potentials; Simulated annealing; Interaction centers; Coarse-grained models; Coiled coils (search for similar items in EconPapers)
Date: 2006
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:371:y:2006:i:2:p:449-462

DOI: 10.1016/j.physa.2006.04.053

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