How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case
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Title
How to Determine Accurate Conformational Ensembles by Metadynamics Metainference: A Chignolin Study Case
Authors
Keywords
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Journal
Frontiers in Molecular Biosciences
Volume 8, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2021-05-26
DOI
10.3389/fmolb.2021.694130
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- (2018) Dan Mendels et al. Journal of Physical Chemistry Letters
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- CHARMM36m: an improved force field for folded and intrinsically disordered proteins
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- Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics
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- PLUMED 2: New feathers for an old bird
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- (2008) Alessandro Barducci et al. PHYSICAL REVIEW LETTERS
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