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Sampling Kinetic Protein Folding Pathways using All-Atom Models

  • P.G. Bolhuis
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Part of the Lecture Notes in Physics book series (LNP, volume 703)

Abstract

This chapter summarizes several computational strategies to study the kinetics of two-state protein folding using all atom models. After explaining the background of two state folding using energy landscapes I introduce common protein models and computational tools to study folding thermodynamics and kinetics. Free energy landscapes are able to capture the thermodynamics of two-state protein folding, and several methods for efficient sampling of these landscapes are presented. An accurate estimate of folding kinetics, the main topic of this chapter, is more difficult to achieve. I argue that path sampling methods are well suited to overcome the problems connected to the sampling of folding kinetics. Some of the major issues are illustrated in the case study on the folding of the GB1 hairpin.

Keywords

Monte Carlo Root Mean Square Deviation Energy Landscape Transition State Theory Free Energy Barrier 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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© Springer 2006

Authors and Affiliations

  • P.G. Bolhuis
    • 1
  1. 1.van ’t Ho. Institute for Molecular SciencesUniversiteit van AmsterdamAmsterdamThe Netherlands

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