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DIALS: New Computational Methods to Enable Challenging Crystallographic Experiments

DIALS：新的计算方法可实现具有挑战性的晶体学实验

基本信息

批准号：
9242823
负责人：
NICHOLAS K SAUTER
金额：
$ 3.15万
依托单位：
UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-03-01 至 2017-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9242823
关键词：
Algorithms Architecture Biochemical Biological Cells Communities Complement Computer software Computing Methodologies Consensus Consumption Coupled Crystallography Data Data Collection Data Set Detection Disease Generations Goals Grant Growth Health Human Image Individual Life Light Maps Measurement Measures Metals Methods Microscopic Modeling Molecular Conformation Molecular Structure Needles Nucleic Acids Pattern Phase Physiologic pulse Physiological Powder dose form Process Proteins Protocols documentation Publications Radiation Reaction Resolution Roentgen Rays Rotation Sampling Scientist Shapes Signal Transduction Source Specimen Spottings Structure Sulfur Synchrotrons Techniques Technology Temperature Testing Time United States National Institutes of Health Work X-Ray Crystallography amyloid peptide base beamline computerized data processing data reduction design detector electron density experimental analysis free-electron laser imaging detector improved instrumentation metalloenzyme open source physical model physical property programs protein structure public health relevance radiation effect research study submicron synchrotron radiation two-dimensional

项目摘要

DESCRIPTION (provided by applicant): Basic biochemical mechanisms fundamental to human health arise from understanding the structure of large biological molecules, both proteins and nucleic acids. X-ray crystallography has been a key method for uncovering their structure and function. This project will develop computational methods needed to enable the use of serial X-ray crystallography techniques. Serial crystallography, performed at either third generation synchrotron beamlines or X-ray free-electron lasers, is emerging as a way to determine molecular structure using crystals that are probed once with a short X-ray pulse and then exchanged for a new sample. This a departure from traditional single-crystal experiments where the crystal is rotated in the beam to assemble a full data set, but which require large crystals, coupled with cryocooling to slow down the effects of radiation damage. Serial crystallography, in contrast, is performed with an extremely short X-ray pulse, which probes the structure before radiation damage occurs, and at normal physiological temperatures, where the full range of available molecular conformations can be revealed. The program DIALS (Diffraction Integration for Advanced Light Sources) reduces crystal diffraction patterns to a list of Bragg spot intensities, which are needed to compute the electron density map leading to an atomic model. Because the diffraction pattern in serial crystallography is sampled from still crystals rather than rotating ones, the analysis of Bragg spot intensities is entirely different. Frst, a correction must be applied to convert the intensity to the equivalent observation from a single rotating crystal, then duplicate Bragg spot measurements from potentially thousands of crystals must be merged to derive a single complete data set. This project will explore the assumptions made during this data reduction process, and identify optimal physical models and algorithms for deriving the best merged data. At the same time, DIALS will be released as a general data reduction package for all synchrotron-based crystallography (for both serial and single-crystal methods). DIALS is built around an open- source, community-oriented software architecture that can be adapted by beamline scientists to accommodate new instrumentation, in a field where rapid hardware advances are expected to continue for many years.