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An independent method for the analysis of protein folding kinetics from all-atom molecular dynamics simulations.

Authors
Type
Published Article
Journal
Journal of biomolecular structure & dynamics
Publication Date
Volume
23
Issue
1
Pages
73–76
Identifiers
PMID: 15918678
Source
Medline
License
Unknown

Abstract

We propose a method for extracting useful kinetic information from all-atom molecular dynamics simulations of protein folding. By calculating the time correlation functions between the evolution of different structural properties during the course of the simulation we can determine the endpoint of the reaction and the mechanism by which it occurs. As a test of our method we use thermal denaturation simulations on a 76 residue protein, ubiquitin. The method we present should be used in combination with current techniques for analyzing molecular dynamics trajectories.

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