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From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
2014 (English)In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 54, no 8-9, 1274-1285 p.Article, review/survey (Refereed) Published
Abstract [en]

Simulations of biological macromolecules have evolved tremendously since the discoveries of the 1970s. The field has moved from simple simulations in vacuo on picosecond scales to milliseconds of accurate sampling of large proteins, and it has become a standard tool in biochemistry and biophysics, rather than a dedicated theoretical one. This is partly due to increasing computational power, but it would not have been possible without huge research efforts invested in new algorithms and software. Here, we illustrate some of this development, both past and future challenges, and in particular, discuss how the recent introduction of modern ensemble methods is breaking the trend of ever-longer simulations to instead focus on throughput and sampling. This has not only helped simulations become much more accurate, but it provides statistical error estimates, which are critical, as simulations are increasingly used to predict properties that have not yet been measured experimentally.

Place, publisher, year, edition, pages
2014. Vol. 54, no 8-9, 1274-1285 p.
Keyword [en]
ensemble simulation, molecular dynamics, parallel adaptive simulation, protein folding, sampling methods
National Category
Biological Sciences Chemical Sciences
Identifiers
URN: urn:nbn:se:su:diva-109052DOI: 10.1002/ijch.201400020ISI: 000342796500022OAI: oai:DiVA.org:su-109052DiVA: diva2:763261
Note

AuthorCount:3;

Available from: 2014-11-14 Created: 2014-11-10 Last updated: 2017-12-05Bibliographically approved

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Lindahl, Erik
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