Simulations of a small protein in a specifically designed generalized ensemble

Document Type

Article

Publication Date

1-1-2004

Abstract

We describe a variant of the generalized-ensemble approach that allows faster simulations for special classes of proteins. We test this technique for an all-atom model of the 36-residue protein HP-36. The dependence of various thermodynamic quantities on small modifications of the solvent representation is explored. Configurations with a root-mean square deviation of less than [Formula presented] to the experimentally determined structure are observed. © 2004 The American Physical Society.

Publication Title

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

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