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SAXS-Guided Metadynamics
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm University, Sweden.ORCID iD: 0000-0002-2734-2794
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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:kth:diva-172178DOI: 10.1021/acs.jctc.5b00299ISI: 000358104800057Scopus ID: 2-s2.0-84949671194OAI: oai:DiVA.org:kth-172178DiVA: diva2:846615
Note

QC 20150817

Available from: 2015-08-17 Created: 2015-08-14 Last updated: 2017-11-15

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Lindahl, ErikAndersson, Magnus

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