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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Kernel Energy Method Applied To Vesicular Stomatitis Virus Nucleoprotein
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Kernel Energy Method Applied To Vesicular Stomatitis Virus Nucleoprotein

机译：核能法在水疱性口炎病毒核蛋白中的应用

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摘要

The kernel energy method (KEM) is applied to the vesicular stomatitis virus (VSV) nucleoprotein (PDB ID code 2QVJ). The calculations employ atomic coordinates from the crystal structure at 2.8-A resolution, except for the hydrogen atoms, whose positions were modeled by using the computer program HYPERCHEM. The calculated KEM ab initio limited basis Hartree-Fock energy for the full 33,175 atom molecule (including hydrogen atoms) is obtained. In the KEM, a full biological molecule is represented by smaller "kernels" of atoms, greatly simplifying the calculations. Collections of kernels are well suited for parallel computation. VSV consists of five similar chains, and we obtain the energy of each chain. Interchain hydrogen bonds contribute to the interaction energy between the chains. These hydrogen bond energies are calculated in Hartree-Fock (HF) and Moller-Plesset perturbation theory to second order (MP2) approximations by using 6-31G basis orbit-als. The correlation energy, included in MP2, is a significant factor in the interchain hydrogen bond energies.
机译：核能法（KEM）被应用于水泡性口炎病毒（VSV）核蛋白（PDB ID码2QVJ）。除了氢原子的位置使用计算机程序HYPERCHEM进行建模之外，计算使用的是来自2.8 A分辨率的晶体结构的原子坐标。获得了完整的33,175个原子分子（包括氢原子）的从头算的KEM从头开始的有限基Hartree-Fock能量。在KEM中，完整的生物分子由较小的原子“核”表示，从而大大简化了计算。内核集合非常适合于并行计算。 VSV由五个相似的链组成，我们获得每个链的能量。链间氢键有助于链之间的相互作用能。这些氢键能通过使用6-31G基本轨道方程在Hartree-Fock（HF）和Moller-Plesset微扰理论中近似为二阶（MP2）近似值。 MP2中包含的相关能是链间氢键能的重要因素。

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