BINDING FREE ENERGIES & EXTRACTION SELECTIVITY CALCULATIONS

结合自由能量

• 批准号: 6119272
• 负责人: JAROSLAV VACEK
• 金额: $ 0.54万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-07-01 至 2000-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6119272
• 关键词: biological products; biomedical resource; model design /development; statistics /biometry; technology /technique

In this research project we are using free energy perturbation molecular dynamics simulations as implemented in AMBER 4.1 and AMBER 5.0 packages to estimate host-guest relative binding free energies of three spherands (spherical organic molecules preorganized for binding) and alkali metal ions (Li+, Na+, K+). Results of this study may be used to improve our ability to predict free energies of binding, which may be useful for computer aided drug design. The simulations were performed both in water and chloroform. Access to molecular graphics at the Computer Graphics Laoratory is essential in this study. During the data preparation stage it is important to position the cation in the middle of the spherand cavity. In some cases we also tried to add various amounts of water into the cavity. Picrate anion interacting with the spherand was introduced to simulate experimental conditions. Proper positioning and docking of these guests into the host would be a very painful process without 3D graphical insight.

在这个研究项目中，我们使用自由能微扰 在AMBER 4.1和AMBER中实现的分子动力学模拟 5.0软件包来估计主-客体相对结合自由能 三个球状体（为结合而预先组织的球形有机分子） 和碱金属离子（Li+、Na+、K+）。 这项研究的结果可能是 用来提高我们预测结合自由能的能力， 可能对计算机辅助药物设计有用。 模拟是 在水和氯仿中进行。 访问分子图形 在计算机图形学实验室是必不可少的，在这项研究中。 期间 在数据准备阶段，重要的是将阳离子定位在 在球体和空腔的中间。 在某些情况下，我们还试图添加 将不同量的水注入腔中。 苦味酸阴离子相互作用 与球体的引入，以模拟实验条件。 正确定位和对接这些客人到主机将是 这是一个非常痛苦的过程，没有3D图形的洞察力。