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SAXS-Guided Metadynamics
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
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Number of Authors: 5
2015 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 7, 3491-3498 p.Article 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, 3491-3498 p.
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Chemical Sciences Physical Sciences
Identifiers
URN: urn:nbn:se:su:diva-119740DOI: 10.1021/acs.jctc.5b00299ISI: 000358104800057OAI: oai:DiVA.org:su-119740DiVA: diva2:849231
Available from: 2015-08-27 Created: 2015-08-24 Last updated: 2017-12-04Bibliographically approved

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Kimanius, DariLindahl, Erik
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