XIPP：多维 NMR 分析软件。
XIPP: multi-dimensional NMR analysis software.
机构信息
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
出版信息
J Biomol NMR. 2020 Jan;74(1):9-25. doi: 10.1007/s10858-019-00286-w. Epub 2019 Nov 20.
Abstract
Here we present the XIPP (eXtensible Interactive Peak Picker) NMR software for analyzing multidimensional NMR data of proteins, DNA, RNA and protein-nucleic acid complexes. XIPP organizes experiments into pre-defined studies and replaces our original PIPP software suite which is no longer supported. Default study types exist for backbone assignment, sidechain assignment, NOE assignment and several relaxation series experiments, used in solution NMR studies. XIPP is written in Java and Jython. The default study types are defined in Jython which can be modified and extended to create new types of studies.
摘要
我们在此介绍 XIPP（可扩展交互式峰提取器） NMR 软件，用于分析蛋白质、DNA、RNA 和蛋白质-核酸复合物的多维 NMR 数据。XIPP 将实验组织到预定义的研究中，并取代了不再受支持的原始 PIPP 软件套件。存在用于在溶液 NMR 研究中使用的骨架分配、侧链分配、NOE 分配和几种弛豫系列实验的默认研究类型。XIPP 是用 Java 和 Jython 编写的。默认的研究类型在 Jython 中定义，可以对其进行修改和扩展，以创建新类型的研究。
相似文献
1
XIPP: multi-dimensional NMR analysis software.XIPP：多维 NMR 分析软件。
J Biomol NMR. 2020 Jan;74(1):9-25. doi: 10.1007/s10858-019-00286-w. Epub 2019 Nov 20.
2
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.使用新软件CANDID和扭转角动力学算法DYANA进行自动NOE归属的蛋白质核磁共振结构测定。
J Mol Biol. 2002 May 24;319(1):209-27. doi: 10.1016/s0022-2836(02)00241-3.
3
Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data.使用无 TOCSY 数据的 RDC 定义骨架进行蛋白质侧链共振分配和 NOE 分配。
J Biomol NMR. 2011 Aug;50(4):371-95. doi: 10.1007/s10858-011-9522-4. Epub 2011 Jun 25.
4
Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.使用新软件ATNOS在NOESY谱中通过自动识别NOE来测定蛋白质核磁共振结构。
J Biomol NMR. 2002 Nov;24(3):171-89. doi: 10.1023/a:1021614115432.
5
Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers.通过 Bruker 光谱仪上的 ADAPT-NMR 实现快速自动化蛋白质 NMR 数据采集和分配。
J Magn Reson. 2013 Nov;236:83-8. doi: 10.1016/j.jmr.2013.08.010. Epub 2013 Aug 30.
6
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules.POKY：用于生物分子多维 NMR 和 3D 结构计算的软件套件。
Bioinformatics. 2021 Sep 29;37(18):3041-3042. doi: 10.1093/bioinformatics/btab180.
7
Automated NMR relaxation dispersion data analysis using NESSY.使用 NESSY 进行自动 NMR 弛豫色散数据分析。
BMC Bioinformatics. 2011 Oct 27;12:421. doi: 10.1186/1471-2105-12-421.
8
NOEnet--use of NOE networks for NMR resonance assignment of proteins with known 3D structure.NOEnet——利用NOE网络对具有已知三维结构的蛋白质进行核磁共振共振归属。
Bioinformatics. 2009 Feb 15;25(4):474-81. doi: 10.1093/bioinformatics/btn638. Epub 2008 Dec 12.
9
Exploiting image registration for automated resonance assignment in NMR.利用图像配准技术实现核磁共振中的自动共振归属
J Biomol NMR. 2015 Jun;62(2):143-56. doi: 10.1007/s10858-015-9926-7. Epub 2015 Apr 1.
10
Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing.使用模拟退火对宏观取向蛋白质的 NMR 谱进行自动分配。
J Magn Reson. 2018 Aug;293:104-114. doi: 10.1016/j.jmr.2018.06.004. Epub 2018 Jun 17.
引用本文的文献
1
Unraveling structural transitions and kinetics along the fold-switching pathway of the RfaH C-terminal domain using exchange-based NMR.利用基于交换的核磁共振技术揭示RfaH C端结构域折叠转换途径中的结构转变和动力学。
Proc Natl Acad Sci U S A. 2025 May 20;122(20):e2506441122. doi: 10.1073/pnas.2506441122. Epub 2025 May 14.
2
Molecular basis of hemoglobin binding and heme removal in .血红蛋白结合及血红素去除的分子基础 于……中 （原文最后似乎不完整）
Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2411833122. doi: 10.1073/pnas.2411833122. Epub 2024 Dec 31.
3
A Transient, Excited Species of the Autoinhibited α-State of the Bacterial Transcription Factor RfaH May Represent an Early Intermediate on the Fold-Switching Pathway.细菌转录因子 RfaH 的自抑制α态的瞬态激发态可能代表折叠转换途径的早期中间态。
Biochemistry. 2024 Aug 20;63(16):2030-2039. doi: 10.1021/acs.biochem.4c00258. Epub 2024 Aug 1.
4
Insight into the autoproteolysis mechanism of the RsgI9 anti-σ factor from Clostridium thermocellum.深入了解热纤梭菌 RsgI9 抗 σ 因子的自水解机制。
Proteins. 2024 Aug;92(8):946-958. doi: 10.1002/prot.26690. Epub 2024 Apr 10.
5
The basal and major pilins in the Corynebacterium diphtheriae SpaA pilus adopt similar structures that competitively react with the pilin polymerase.白喉棒状杆菌 SpaA 菌毛的基础和主要菌毛采用类似的结构，与菌毛聚合酶竞争反应。
Biopolymers. 2024 Jan;115(1):e23539. doi: 10.1002/bip.23539. Epub 2023 May 25.
本文引用的文献
1
CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis.CcpNmr分析分配：一个用于综合核磁共振分析的灵活平台。
J Biomol NMR. 2016 Oct;66(2):111-124. doi: 10.1007/s10858-016-0060-y. Epub 2016 Sep 23.
2
The energetics of a three-state protein folding system probed by high-pressure relaxation dispersion NMR spectroscopy.通过高压弛豫色散核磁共振光谱探测的三态蛋白质折叠系统的能量学。
Angew Chem Int Ed Engl. 2015 Sep 14;54(38):11157-61. doi: 10.1002/anie.201505416.
3
Intrinsic unfoldase/foldase activity of the chaperonin GroEL directly demonstrated using multinuclear relaxation-based NMR.利用基于多核弛豫的核磁共振直接证明伴侣蛋白GroEL的内在解折叠酶/折叠酶活性。
Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8817-23. doi: 10.1073/pnas.1510083112. Epub 2015 Jun 29.
4
Visualizing transient dark states by NMR spectroscopy.通过核磁共振光谱法可视化瞬态暗态。
Q Rev Biophys. 2015 Feb;48(1):35-116. doi: 10.1017/S0033583514000122.
5
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.NMRFAM-SPARKY：用于生物分子核磁共振光谱学的增强软件。
Bioinformatics. 2015 Apr 15;31(8):1325-7. doi: 10.1093/bioinformatics/btu830. Epub 2014 Dec 12.
6
The program XEASY for computer-supported NMR spectral analysis of biological macromolecules.用于生物大分子的计算机支持的 NMR 光谱分析的 XEASY 程序。
J Biomol NMR. 1995 Jul;6(1):1-10. doi: 10.1007/BF00417486.
7
NMR View: A computer program for the visualization and analysis of NMR data.NMR 视图：用于可视化和分析 NMR 数据的计算机程序。
J Biomol NMR. 1994 Sep;4(5):603-14. doi: 10.1007/BF00404272.
8
A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams. 1991.一种使用等高线图自动计算机分析在二维、三维和四维光谱中进行峰挑选的常识性方法。1991年。
J Magn Reson. 2011 Dec;213(2):357-63. doi: 10.1016/j.jmr.2011.09.007.
9
Automatic assignment of the intrinsically disordered protein Tau with 441-residues.自动分配具有 441 个残基的 Tau 蛋白。
J Am Chem Soc. 2010 Sep 1;132(34):11906-7. doi: 10.1021/ja105657f.
10
The CCPN data model for NMR spectroscopy: development of a software pipeline.用于核磁共振波谱的CCPN数据模型：软件流程的开发
Proteins. 2005 Jun 1;59(4):687-96. doi: 10.1002/prot.20449.
Zotero 插件