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Articles

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

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Pages 1046-1055 | Received 01 Sep 2015, Accepted 14 Nov 2015, Published online: 05 Jul 2016

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Crossref
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Crossref
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Crossref
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Crossref
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Th?r?se Malliavin. (2017) Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics. Toxins 9:7, pages 199.
Crossref
Bradley M Dickson. (2017) Survey of adaptive biasing potentials: comparisons and outlook. Current Opinion in Structural Biology 43, pages 63-67.
Crossref
Yinglong Miao & J. Andrew McCammon. 2017. 231 278 .

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