基于接触的粗粒化模型中结构化和无序蛋白质的分子动力学：固定接触、可切换接触及由赝非正则二面角描述的接触
Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles
AI总结：
本文提出一种基于Cα的粗粒化蛋白质模型，结合类Go势和两种可转移无序区势（动态结构接触与赝非正则二面角势），可高效模拟毫秒尺度下数千残基的结构化与无序蛋白质。
摘要：
我们提出了一种基于C$α$的粗粒化蛋白质模型，可用于模拟结构化、固有无序和部分无序的蛋白质。我们对结构化部分采用类Go势，对无序部分采用两种不同的可转移势变体。第一种变体使用动态基于结构的（DSB）接触，这些接触在模拟过程中准绝热地形成和消失。通过使用特定的结构判据，我们区分了侧链-侧链、侧链-主链和主链-主链接触。第二种变体是一种非径向多体赝非正则二面角（PID）势，它不包含时间相关项，但需要更多的计算资源。我们的模型能够在合理的时间内模拟毫秒时间尺度上数千个残基。
英文摘要：
We present a coarse-grained C$α$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of a transferable potential for the disordered parts. The first variant uses dynamic structure-based (DSB) contacts that form and disappear quasi-adiabatically during the simulation. By using specific structural criteria we distinguish sidechain-sidechain, sidechain-backbone and backbone-backbone contacts. The second variant is a non-radial multi-body pseudo-improper-dihedral (PID) potential that does not include time-dependent terms but requires more computational resources. Our model can simulate in reasonable time thousands of residues on millisecond time scales.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
