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An efficient method has been developed for packing alpha-helices in proteins. It treats alpha-helices as rigid bodies and uses a simplified Lennard-Jones potential with Miyazawa-Jernigan contact-energy parameters to describe the interactions between the alpha-helical elements in this coarse-grained system. Global conformational searches to generate packing arrangements rapidly are carried out with a Monte Carlo-with-minimization type of approach. The results for 42 proteins show that the approach reproduces native-like folds of alpha-helical proteins as low-energy local minima of this highly simplified potential function.
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Nanias et al. (2003) studied this question.
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