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Towards a General Probabilistic Model of Protein Structure: The Reference Ratio Method

  • Jes Frellsen
  • Kanti V. Mardia
  • Mikael Borg
  • Jesper Ferkinghoff-Borg
  • Thomas Hamelryck
Chapter
Part of the Statistics for Biology and Health book series (SBH)

Abstract

The recently introduced reference ratio method[276] allows combining distributions over fine-grained variables with distributions over coarse-grained variables in a meaningful way. This problem is a major bottleneck in the prediction, simulation and design of protein structure and dynamics. Hamelryck et al. [276] introduced the reference ratio method in this context, and showed that the method provides a rigorous statistical explanation of the so called potentials of mean force(PMFs). These potentials are widely used in protein structure prediction and simulation, but their physical justification is highly disputed [32, 390, 715]. The reference ratio method clarifies, justifies and extends the scope of these potentials.

Notes

Acknowledgements

The authors acknowledge funding by the Danish Research Council for Technology and Production Sciences (FTP, project: Protein structure ensembles from mathematical models, 09-066546).

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Jes Frellsen
    • 1
  • Kanti V. Mardia
    • 2
  • Mikael Borg
    • 1
  • Jesper Ferkinghoff-Borg
    • 3
  • Thomas Hamelryck
    • 1
  1. 1.The Bioinformatics CentreUniversity of CopenhagenCopenhagenDenmark
  2. 2.Department of StatisticsUniversity of LeedsLeedsUK
  3. 3.Department of Electrical EngineeringTechnical University of DenmarkLyngbyDenmark

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