Wan Shunzhou, Coveney Peter V, Flower Darren R
Centre for Computational Science, Department of Chemistry, University College London, UK.
Philos Trans A Math Phys Eng Sci. 2005 Aug 15;363(1833):2037-53. doi: 10.1098/rsta.2005.1627.
The binding to the T cell receptor of wild-type and variant HTLV-1 Tax peptide complexed to the major histocompatibility complex has been investigated by means of molecular dynamics simulations. The binding free energy difference is calculated using the molecular mechanics Poisson-Boltzmann surface area and linear interaction energy methods. These methods extract useful information on the binding energetics from simulations of the physical states of the ligands, which are more computationally expedient than the commonly used thermodynamic integration method. The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines.
通过分子动力学模拟研究了与主要组织相容性复合体复合的野生型和变异型人嗜T淋巴细胞病毒1型（HTLV-1）Tax肽与T细胞受体的结合。使用分子力学泊松-玻尔兹曼表面积和线性相互作用能方法计算结合自由能差。这些方法从配体物理状态的模拟中提取有关结合能学的有用信息，这比常用的热力学积分方法在计算上更简便。相对结合自由能的成功再现表明，这些方法可用于自由能计算以及药物和疫苗的合理设计。
