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评论“人类血红蛋白的有效分子动力学模拟需要一个惊人的大盒子尺寸”。

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

机构信息

Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.

出版信息

Elife. 2019 Jun 20;8:e44718. doi: 10.7554/eLife.44718.

Abstract

A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

摘要

最近一项关于血红蛋白稳定性的分子动力学研究得出结论,当模拟中使用的溶剂盒比通常使用的溶剂盒大十倍时,未配位的蛋白质仅在 T 态下稳定(El Hage 等人,2018 年)。在这里,我们对该研究表达了三个主要关注。此外,我们发现,使用数量级更多的统计数据,报告的盒尺寸依赖性不可重现。总体而言,未观察到构象转变的动力学或热力学有任何显著影响。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ea58/6586461/c011cc362aff/elife-44718-fig1.jpg

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