Why are MD simulated protein folding times wrong?

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The question of significant deviations of protein folding times simulated using molecular dynamics from experimental values is investigated. It is shown that in the framework of Markov State Model (MSM) describing the conformational dynamics of peptides and proteins, the folding time is very sensitive to the simulation model parameters, such as forcefield and temperature. Using two peptides as examples, we show that the deviations in the folding times can reach an order of magnitude for modest variations of the molecular model. We, therefore, conclude that the folding rate values obtained in molecular dynamics simulations have to be treated with care.
Original languageEnglish
Title of host publicationAdvances in Computational Biology
EditorsHamid R. Arabnia
PublisherSpringer
Pages321-326
Number of pages6
VolumePart 3
ISBN (Print)9781441959126
DOIs
Publication statusPublished - 6 Oct 2010

Publication series

NameAdvances in Experimental Medicine and Biology
PublisherSpringer
Volume680

Bibliographical note

The original publication is available at www.springerlink.com

Keywords

  • molecular dynamics
  • MSM
  • protein folding
  • simulation models
  • VPAL

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