DichroCalc: DNA Dichroism Calculations

1953年，克里克和沃森从富兰克林、高斯林和威尔金斯的X射线数据中破译了DNA的结构，从而奠定了现代分子生物学和分子医学的基础。理解DNA结构在20世纪和21世纪所产生的影响--科学、医学和经济--几乎不可能被夸大。在这个提议中，我们试图提供一个计算工具，用于将DNA在溶液中的结构与测量DNA与偏振光相互作用的生物物理实验联系起来。这样的实验可以补充其他方法，使用NMR或红外光谱。探测DNA与其他分子结合时的构象提供了有关其与其他分子相互作用的宝贵信息，可能是理解分子生物学核心的大量过程的第一步。尽管与光谱学结构相关的完全定量理论的重要性很明显，但这样的理论尚未实现。在过去的十年中，诺丁汉发展的专业知识使我们几乎处于独特的有利地位，可以推进精确计算DNA光谱所需的理论。这将涉及在诺丁汉的12万亿次高性能计算机（HPC）上进行量子化学计算。此外，我们的网络服务器DichroCalc是世界上唯一一个科学家可以上传生物大分子结构并返回计算的圆二色光谱的服务器。因此，我们将能够很容易地传播研究成果，并以易于使用的方式向科学研究界提供这些成果。

In 1953, Crick and Watson deciphered the structure of DNA from the X-ray data of Franklin, Gosling and Wilkins, thereby laying the foundation of modern day molecular biology and molecular medicine. It is almost impossible to overstate the impact - scientific, medical and economic - that understanding the structure of DNA has had in the 20th and 21st centuries. In this proposal, we seek to provide a computational tool for relating the structure of DNA in SOLUTION to biophysical experiments that measure the interaction of DNA with polarized light. Such experiments can complement other approaches, using NMR or infrared spectroscopy. Probing the conformation of DNA as its binds other molecules provides valuable information on its interactions with other molecules and could be the first step in understanding a huge range of processes at the heart of molecular biology. Despite the clear importance of a fully quantitative theory relating structure to optical spectroscopy, such a theory has yet to be realized. Expertise developed at Nottingham over the past decade makes us almost uniquely well-placed to advance the theory necessary to calculate the optical spectroscopy of DNA accurately. This will involve quantum chemical calculations on Nottingham's 12-teraflop high performance computer (HPC). In addition, our web-server, DichroCalc, is the only one world-wide, where scientists can upload biological macromolecular structures and get back a calculated circular dichroism spectrum. Thus, we will be able to disseminate the results of research quite readily and make them accessible to the scientific research community in an-easy-to-use fashion.