National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA.
NetSeer, Inc, 555 Ellis Street, Suite B, Mountain View, CA, 94043, USA.
J Biomol NMR. 2019 May;73(5):213-222. doi: 10.1007/s10858-019-00255-3. Epub 2019 Jun 4.
Various methods for understanding the structural and dynamic properties of proteins rely on the analysis of their NMR chemical shifts. These methods require the initial assignment of NMR signals to particular atoms in the sequence of the protein, a step that can be very time-consuming. The probabilistic interaction network of evidence (PINE) algorithm for automated assignment of backbone and side chain chemical shifts utilizes a Bayesian probabilistic network model that analyzes sequence data and peak lists from multiple NMR experiments. PINE, which is one of the most popular and reliable automated chemical shift assignment algorithms, has been available to the protein NMR community for longer than a decade. We announce here a new web server version of PINE, called Integrative PINE (I-PINE), which supports more types of NMR experiments than PINE (including three-dimensional nuclear Overhauser enhancement and four-dimensional J-coupling experiments) along with more comprehensive visualization of chemical shift based analysis of protein structure and dynamics. The I-PINE server is freely accessible at http://i-pine.nmrfam.wisc.edu . Help pages and tutorial including browser capability are available at: http://i-pine.nmrfam.wisc.edu/instruction.html . Sample data that can be used for testing the web server are available at: http://i-pine.nmrfam.wisc.edu/examples.html .
各种理解蛋白质结构和动态特性的方法都依赖于对其 NMR 化学位移的分析。这些方法需要将 NMR 信号初始分配给蛋白质序列中特定的原子，这一步可能非常耗时。用于自动分配骨架和侧链化学位移的概率交互网络证据 (PINE) 算法利用贝叶斯概率网络模型分析来自多个 NMR 实验的序列数据和峰列表。PINE 是最流行和可靠的自动化学位移分配算法之一，已经在蛋白质 NMR 社区中使用了十多年。我们在这里宣布 PINE 的一个新的网络服务器版本，称为综合 PINE（I-PINE），它支持比 PINE 更多类型的 NMR 实验（包括三维核 Overhauser 增强和四维 J 耦合实验），以及更全面的基于化学位移的蛋白质结构和动力学分析的可视化。I-PINE 服务器可在 http://i-pine.nmrfam.wisc.edu 免费访问。帮助页面和教程，包括浏览器功能，可在：http://i-pine.nmrfam.wisc.edu/ instruction.html 获得。可用于测试网络服务器的示例数据可在：http://i-pine.nmrfam.wisc.edu/examples.html 获得。
