National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin - Madison, Madison, Wisconsin, United States of America.
PLoS One. 2012;7(3):e33173. doi: 10.1371/journal.pone.0033173. Epub 2012 Mar 12.
ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) represents a groundbreaking prototype for automated protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. With a [(13)C,(15)N]-labeled protein sample loaded into the NMR spectrometer, ADAPT-NMR delivers complete backbone resonance assignments and secondary structure in an optimal fashion without human intervention. ADAPT-NMR achieves this by implementing a strategy in which the goal of optimal assignment in each step determines the subsequent step by analyzing the current sum of available data. ADAPT-NMR is the first iterative and fully automated approach designed specifically for the optimal assignment of proteins with fast data collection as a byproduct of this goal. ADAPT-NMR evaluates the current spectral information, and uses a goal-directed objective function to select the optimal next data collection step(s) and then directs the NMR spectrometer to collect the selected data set. ADAPT-NMR extracts peak positions from the newly collected data and uses this information in updating the analysis resonance assignments and secondary structure. The goal-directed objective function then defines the next data collection step. The procedure continues until the collected data support comprehensive peak identification, resonance assignments at the desired level of completeness, and protein secondary structure. We present test cases in which ADAPT-NMR achieved results in two days or less that would have taken two months or more by manual approaches.
ADAPT-NMR（利用 NMR 中的概率工具包进行定向数据收集的算法）代表了通过核磁共振（NMR）光谱自动确定蛋白质结构的开创性原型。将 [(13)C，(15)N]-标记的蛋白质样品加载到 NMR 光谱仪中，ADAPT-NMR 以最佳方式提供完整的骨架共振分配和二级结构，而无需人工干预。ADAPT-NMR 通过实施一种策略来实现这一点，在该策略中，每个步骤中最佳分配的目标通过分析当前可用数据的总和来确定后续步骤。ADAPT-NMR 是第一个迭代和完全自动化的方法，专门设计用于快速数据收集的蛋白质的最佳分配，这是该目标的副产品。ADAPT-NMR 评估当前的光谱信息，并使用目标导向的目标函数选择最佳的下一步数据采集步骤，然后指导 NMR 光谱仪采集所选数据集。ADAPT-NMR 从新收集的数据中提取峰位置，并在更新分析共振分配和二级结构时使用此信息。目标导向的目标函数然后定义下一个数据采集步骤。该过程一直持续到收集的数据支持全面的峰识别、所需完整程度的共振分配以及蛋白质二级结构。我们展示了 ADAPT-NMR 在两天或更短的时间内实现结果的测试案例，而手动方法则需要两个月或更长时间。
