Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
- Cavalli, Andrea Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom - Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland
- Camilloni, Carlo Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland
- Vendruscolo, Michele Institute for Research in Biomedicine (IRB), Faculty of Biomedical Sciences, Università della Svizzera italiana, Switzerland
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07.03.2013
Published in:
- The journal of chemical physics. - 2013, vol. 138, no. 9, p. 094112
English
In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.
- Language
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- English
- Classification
- Medicine
- License
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License undefined
- Open access status
- green
- Identifiers
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- RERO DOC 324251
- DOI 10.1063/1.4793625
- ARK ark:/12658/srd1318872
- Persistent URL
- https://n2t.net/ark:/12658/srd1318872
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