Publications by authors named "Lauren E Raguette"
Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids.
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- RNA research is expanding, but understanding its structural dynamics and interactions with small molecules remains limited, especially when compared to protein studies.
- This study focuses on addressing the weak CH···O interactions in RNA, which are significant yet often overlooked in force field development, particularly in widely used Amber RNA force fields.
- By adjusting the CH···O repulsion in these force fields, the study found that RNA simulations became more stable, resulting in improved accuracy in modeling RNA structures during molecular dynamics simulations.