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.

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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