Optimized Folding Simulations of Protein A
arXiv:0711.3830 · doi:10.1140/epje/i2007-10241-1
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 approximately 3A to the experimentally determined structure (Protein Data Bank identifier 1BDD) are found. However, at biologically relevant temperatures such conformations appear with only about 10% frequency in our simulations. Possible short comings in our energy function are discussed.
6 pages, 8 figures
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