Abstract.
We describe optimized parallel tempering simulations of the 46-residue B-fragment of protein A. Native-like configurations with a root-mean-square deviation of ≈ 3 Å to the experimentally determined structure (Protein Data Bank identifier 1BDD) are found. However, at biologically relevant temperatures such conformations appear with only ≈ 10 % frequency in our simulations. Possible shortcomings in our energy function are discussed.
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Trebst, S., Hansmann, U.H.E. Optimized folding simulations of protein A. Eur. Phys. J. E 24, 311–316 (2007). https://doi.org/10.1140/epje/i2007-10241-1
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DOI: https://doi.org/10.1140/epje/i2007-10241-1