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Quantum-mechanics-derived 13Cα chemical shift server (CheShift) for protein structure validation
Jorge A. Vila et al.
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Berk Hess et al.
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Yang Shen et al.
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Nikola Trbovic et al.
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BioMagResBank
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Scott A. Showalter et al.
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Limits on variations in protein backbone dynamics from precise measurements of scalar couplings
Beat Vogeli et al.
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Yang Shen et al.
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Phineus R. L. Markwick et al.
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M Buck et al.
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D Van der Spoel et al.
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MV Berjanskii et al.
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K Lindorff-Larsen et al.
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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
Y Duan et al.
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S Neal et al.
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RefDB: A database of uniformly referenced protein chemical shifts
HY Zhang et al.
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FL Zhang et al.
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Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins
J Meiler et al.
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GROMACS 3.0: a package for molecular simulation and trajectory analysis
E Lindahl et al.
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The Protein Data Bank
HM Berman et al.
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