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The European Physical Journal E

, Volume 24, Issue 3, pp 311–316 | Cite as

Optimized folding simulations of protein A

  • S. Trebst
  • U. H. E. Hansmann
Regular Article

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.

PACS.

87.14.Ee Proteins 87.15.Aa Theory and modeling; computer simulation 87.15.He Dynamics and conformational changes 87.15.Cc Folding and sequence analysis 

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Copyright information

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

Authors and Affiliations

  1. 1.Microsoft Research, Station QUniversity of CaliforniaSanta BarbaraUSA
  2. 2.Department of PhysicsMichigan Technological UniversityHoughtonUSA
  3. 3.John-von-Neumann Institute for ComputingForschungszentrum JülichJülichGermany

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