Towards real-time XFEL data reduction with CCTBX

描述(申请人提供)：至1995年间艾滋病病毒蛋白水解酶抑制剂药物的快速发展是结构生物学的早期成功故事。结构生物学研究生物分子的三维结构。在艾滋病毒感染周期中至关重要的一种分子结构于1989年首次发表。仅仅六年后，第一批针对这种分子的药物出现在市场上，导致艾滋病死亡率大幅下降。在此后的15年里，药物开发总体上变得越来越依赖结构生物学。对病原体分子结构的了解通常会提出扰乱其功能的方法。与传统的试错方法相比，这可以省去数年的开发时间，并节省数百万美元的开发成本。-获得分子结构的主要方法是X射线结晶学，它占目前已知的所有生物结构的87%。NIH对工业规模的研究设施的长期大规模投资使每年解决的结构数量增加到近10,000个。不幸的是，某些非常重要的分子很难用目前的X射线技术来解决。这些是膜蛋白，市场上60%以上的药物都是以它们为靶标的。据估计，人体内有5,500-7,700种膜蛋白，但目前已知的不到12种结构。这主要是因为众所周知，膜蛋白很难结晶。没有足够大小的晶体，常规的X射线结晶学是不可能的。-最近，出现了一项新的主要X射线技术，有望将研究范围扩大到膜蛋白。世界上第一台硬X射线自由电子激光器(XFEL)的建造于2009年完成。关于膜蛋白质的探索性XFEL工作的第一次出版出现在2011年2月。XFEL仪器可以处理比传统实验所需尺寸小得多的晶体，即使是膜蛋白也可以达到这种尺寸。然而，从XFEL实验中提取结构信息目前需要数月时间。在所有案例中，约28%的XFEL数据处理面临歧义，这阻碍了高质量结果的提取，损害了生物学解释。为了实现XFEL实验的全部潜力，数据处理时间需要减少至少两个数量级，并且需要解决模糊性。-我们拥有为传统X射线实验开发数据处理软件的丰富经验，并在计算晶体工具箱(CCTBX)中实现了开源。在我们国际公认的专业知识和CCTBX的大量模块化工具的基础上，我们将实施XFEL数据的实时处理。这将包括解决数据中的模棱两可的问题，以便高质量的结构信息对于所有类型的药物相关分子都是触手可及的。

DESCRIPTION (provided by applicant): The rapid development of HIV protease inhibitor drugs between 1989 and 1995 is an early success story of structural biology. Structural biology is concerned with three-dimensional structures of biological molecules. The structure of a molecule crucial in the infectious cycle of HIV was first published in 1989. Only six years later the first drugs targeting this molecule appeared on the market, leading to a dramatic decrease in the death rate from AIDS. In the 15 years since, drug development in general has become increasingly dependent on structural biology. Knowledge of the molecular structure of pathogens often suggests ways to disrupt their function. Compared to the traditional trial-and-error approach this can eliminate years of development time and cut many millions of dollars in development costs. - The predominant method for obtaining molecular structures is X-ray crystallography, which accounts for 87% of all biological structures known today. Long-term large-scale investments by NIH into research facilities of industrial dimensions have increased the number of structures solved per year to nearly 10,000. Unfortunately, certain highly important molecules are difficult to solve with current X-ray techniques. These are the membrane proteins, which are the targets of more than 60% of the drugs on the market. There is an estimated 5,500-7,700 membrane proteins in the human body, but fewer than a dozen structures of these are currently known. This is mainly because membrane proteins are notoriously difficult to crystallize. Without crystals of sufficient size conventional X-ray crystallography is impossible. - Very recently, a new major X-ray technology has emerged that promises to expand the reach to membrane proteins. The construction of the world's first hard X-ray Free Electron Laser (XFEL) was completed in 2009. The first publication of exploratory XFEL work on a membrane protein appeared in February 2011. An XFEL instrument can work with crystals of much smaller sizes than are needed for conventional experiments, sizes attainable even with membrane proteins. However, extracting structural information from an XFEL experiment currently takes many months. In about 28% of all cases, XFEL data processing is faced with ambiguities that prevent the extraction of high-quality results, compromising biological interpretation. For XFEL experiments to realize their full potential, the data processing times need to be decreased by at least two orders of magnitude and the ambiguities need to be resolved. - We have extensive experience developing data processing software for conventional X-ray experiments, with open-source implementations in the Computational Crystallography Toolbox (CCTBX). Building on our internationally recognized expertise and the large set of modular tools in CCTBX, we will implement real-time processing of XFEL data. This will include resolving ambiguities in the data if present, so that high-quality structural information will be within reach for all types of pharmaceutically relevant molecules.