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SAXS-Guided Metadynamics
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2015 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 7, p. 3491-3498Article in journal (Refereed) Published
Abstract [en]

The small-angle X-ray scattering (SAXS) methodology enables structural characterization of biological macromolecules in solution. However, because SAXS provides low-dimensional information, several potential structural configurations can reproduce the experimental scattering profile, which severely complicates the structural refinement process. Here, we present a bias-exchange metadynamics refinement protocol that incorporates SAXS data as collective variables and therefore tags all possible configurations with their corresponding free energies, which allows identification of a unique structural solution. The method has been implemented in PLUMED and combined with the GROMACS simulation package, and as a proof of principle, we explore the Trp-cage protein folding landscape.

Place, publisher, year, edition, pages
2015. Vol. 11, no 7, p. 3491-3498
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Chemical Sciences Physical Sciences
Identifiers
URN: urn:nbn:se:umu:diva-153199DOI: 10.1021/acs.jctc.5b00299ISI: 000358104800057Scopus ID: 2-s2.0-84949671194OAI: oai:DiVA.org:umu-153199DiVA, id: diva2:1261890
Note

QC 20150817

Available from: 2018-11-08 Created: 2018-11-08 Last updated: 2018-11-09Bibliographically approved

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fulltext(4591 kB)53 downloads
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Andersson, Magnus

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Lindahl, ErikAndersson, Magnus
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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf