Water dispersion interactions strongly influence simulated structural properties of disordered protein states.

By Stefano Piana, A. Donchev, Paul Robustelli, David E. Shaw. Journal of Physical Chemistry B, 2015

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Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “107,112,113 117 While the sampling of disordered peptides is less relevant in the context of structure re ﬁ nement, which generally targets well-folded proteins, a better balance between folded and disordered states may bene ﬁ t the sampling of more dynamic regions such as longer loops that are…”
Prediction of protein disorder based on IUPred (2018, background): “27 A more robust way to characterize protein structures relies on empirical or knowledge based force fields.”
Developing a molecular dynamics force field for both folded and disordered protein states (2018, methodology): “Our study of multiple popular force fields and water models (7), for example, showed that all tested combinations produced disordered states that were substantially more compact than estimated from experiments.”
Sequence determinants of protein phase behavior from a coarse-grained model (2017, methodology): “All-atom simulation has the potential of fulfilling both 51 tasks [41,42] with the use of force fields suitable for intrinsically disordered proteins 52 (IDPs) [43,44].”
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity (2020, neutral): “The proteins were solvated in TIP4P-D water 53 with 150 mM NaCl.”