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Title
Molecular dynamics simulations of macromolecular crystals
Authors
Keywords
-
Journal
Wiley Interdisciplinary Reviews-Computational Molecular Science
Volume -, Issue -, Pages e1402
Publisher
Wiley
Online
2018-11-17
DOI
10.1002/wcms.1402
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- (2016) Kartik Ayyer et al. NATURE
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- (2016) Andrew H. Van Benschoten et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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