Optimized folding simulations of protein A

Document Type

Article

Publication Date

11-1-2007

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. © 2007 EDP Sciences, Società Italiana di Fisica and Springer-Verlag.

Publication Title

European Physical Journal E

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