Discrete molecular dynamics studies of the folding of a protein-like model
Discrete molecular dynamics studies of the folding of a protein-like model
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DOI：
10.1016/s1359-0278(98)00072-8
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发表时间：
1998-01-01
期刊：
影响因子：
--
通讯作者：
Shakhnovich, EI
中科院分区：
文献类型：
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作者：
Dokholyan, NV;Buldyrev, SV;Shakhnovich, EI
背景：在计算机模拟中，已经进行了许多尝试来及时解决模型蛋白质的折叠。出现了不同的计算方法。这些方法中的一些遭受不敏感的蛋白质的几何特性（晶格模型），而其他的计算量大（传统的分子动力学）。结果：我们使用最近提出的周和Karplus的方法来研究折叠的蛋白质模型的基础上的离散时间分子动力学算法。我们表明，该算法解决了相对于时间的折叠可逆箭头展开过渡。此外，我们证明了研究核心的模型protein.Conclusions：该算法沿着与模型的interresidue相互作用可以作为一种工具，用于研究蛋白质模型的热力学和动力学。
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from insensitivity to the geometrical properties of the proteins (lattice models), whereas others are computationally heavy (traditional molecular dynamics).Results: We used the recently proposed approach of Zhou and Karplus to study the folding of a protein model based on the discrete time molecular dynamics algorithm. We show that this algorithm resolves with respect to time the folding reversible arrow unfolding transition. In addition, we demonstrate the ability to study the core of the model protein.Conclusions: The algorithm along with the model of interresidue interactions can serve as a tool for studying the thermodynamics and kinetics of protein models.