CCPN - A Collaborative computational project for macromolecular NMR spectroscopy

CCPN - 大分子核磁共振波谱的协作计算项目

• 批准号: BB/H004130/1
• 负责人: Ernest Laue
• 金额: $ 118.22万
• 依托单位: University of Cambridge
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FH004130%2F1
• 关键词: CCPN; Collaborative; computational; project; macromolecular

The CCPN is a Collaborative Computing Project for the study of biological macromolecules and the determination of their structures by NMR spectroscopy. Our aim is to promote collaboration between NMR software developers and to make better software available to the NMR user community. Our goal is to ensure that the different computer programs used by NMR spectroscopists work together and use each others' results in a seamless fashion. Secondly, we want to make sure that all the experimental results can easily be collated and made available to others. We also arrange meetings and workshops to define, and spread knowledge about the best ways of carrying out NMR studies. Since the CCPN started in 2000, we have defined a standard way of describing scientific data in our particular area. We have developed large program libraries to make it easier to write programs that read and write data in this standard form. We have also written a new program for the analysis of NMR spectra, and we have worked with other groups to adapt their programs to use data defined in this standard way. It is now possible to determine the structure of a protein by NMR spectroscopy, using only programs that use data in this standard form. We have additionally written programs to make it easier to write and maintain both the data standard and its program libraries, and we have arranged workshops and annual conferences. The new application has five main aims: 1. We want to provide a program to process raw NMR data that uses the data standard, organised so that it can be used to process NMR data in different ways and so that it is easy to add new methods. 2. We want to collaborate with other groups to expand the support for different types of NMR analysis. Among other things we shall be adding support for solid state NMR studies, and we will collaborate with two pharmaceutical companies to write programs that can be used in small molecule screening and optimisation by NMR spectroscopy. 3. In collaboration with others we want to combine the programs that interact with the data standard into a tightly integrated software pipeline where the programs speak directly to each other, and where you can compare the use of different programs for the same task. The entire pipeline should be easy to install, and parts of it will be made available and run as web services. At the end of the grant we hope to be able to run the pipeline in a fully automatic mode, so that one can generate a structure automatically, directly from the raw NMR data. 4. We shall continue to support our existing users, improve our documentation and maintain the large amounts of code we have already written. 5. And we shall continue to arrange courses, workshops and annual conferences. Our work helps those who use NMR spectroscopy by providing programs that are more powerful and easier to use and install. It also makes it easier to write those programs, and saves effort by letting new programs make better use of existing code. Ultimately we shall increase both the amount and quality of experimental NMR data that is deposited in public databanks and made available to others. More specifically we hope to make our programs more widely used in industry by adding support for industry-relevant tasks, and to make macromolecular NMR data sufficiently simple to analyse that it can be done by non-specialists without excessive training.

CCPN是一个合作计算项目，用于研究生物大分子并通过NMR光谱确定其结构。我们的目标是促进NMR软件开发人员之间的合作，并为NMR用户社区提供更好的软件。我们的目标是确保核磁共振波谱仪使用的不同计算机程序能够协同工作，并以无缝的方式使用彼此的结果。第二，我们要确保所有的实验结果可以很容易地整理和提供给其他人。我们还安排会议和研讨会，以确定和传播有关开展NMR研究的最佳方式的知识。自2000年CCPN成立以来，我们已经定义了一种描述特定领域科学数据的标准方法。我们已经开发了大型程序库，以使编写以这种标准形式读取和写入数据的程序变得更容易。我们还编写了一个新的核磁共振谱分析程序，并与其他小组合作，使他们的程序能够使用这种标准方法定义的数据。现在可以通过NMR光谱法确定蛋白质的结构，只使用使用这种标准形式的数据的程序。我们还编写了程序，使数据标准及其程序库的编写和维护更加容易，我们还安排了研讨会和年度会议。新的应用程序有五个主要目标：1。我们希望提供一个程序来处理使用数据标准的原始NMR数据，组织起来，以便它可以用于以不同的方式处理NMR数据，并且很容易添加新方法。2.我们希望与其他团体合作，扩大对不同类型NMR分析的支持。除此之外，我们将增加对固态NMR研究的支持，我们将与两家制药公司合作编写可用于NMR光谱法小分子筛选和优化的程序。3.通过与其他人的合作，我们希望将与数据标准交互的程序联合收割机组合到一个紧密集成的软件管道中，在这个管道中，程序可以直接相互交流，并且可以比较不同程序对同一任务的使用。整个管道应该很容易安装，部分管道将作为Web服务提供和运行。在拨款结束时，我们希望能够以全自动模式运行管道，以便可以直接从原始NMR数据自动生成结构。4.我们将继续支持我们现有的用户，改进我们的文档，并维护我们已经编写的大量代码。5.我们将继续安排课程、讲习班和年度会议。我们的工作通过提供更强大、更易于使用和安装的程序来帮助那些使用NMR光谱的人。它还使编写这些程序变得更容易，并通过让新程序更好地利用现有代码来节省工作量。最终，我们将提高存放在公共数据库中并提供给他人的实验NMR数据的数量和质量。更具体地说，我们希望通过增加对工业相关任务的支持，使我们的程序在工业中得到更广泛的应用，并使大分子NMR数据足够简单，可以由非专业人员在没有过多培训的情况下进行分析。

项目成果

Straightforward and complete deposition of NMR data to the PDBe.

• DOI: 10.1007/s10858-010-9439-3
• 发表时间: 2010-10
• 期刊: Journal of biomolecular NMR
• 影响因子: 2.7
• 作者: Penkett CJ;van Ginkel G;Velankar S;Swaminathan J;Ulrich EL;Mading S;Stevens TJ;Fogh RH;Gutmanas A;Kleywegt GJ;Henrick K;Vranken WF
• 通讯作者: Vranken WF

Fragment-Based Drug Discovery by NMR. Where Are the Successes and Where can It Be Improved?

• DOI: 10.3389/fmolb.2022.834453
• 发表时间: 2022
• 期刊: Frontiers in molecular biosciences
• 影响因子: 5
• 作者: Mureddu LG;Vuister GW
• 通讯作者: Vuister GW

Analysis of the structural quality of the CASD-NMR 2013 entries.

• DOI: 10.1007/s10858-015-9949-0
• 发表时间: 2015-08
• 期刊: Journal of biomolecular NMR
• 影响因子: 2.7
• 作者: Ragan TJ;Fogh RH;Tejero R;Vranken W;Montelione GT;Rosato A;Vuister GW
• 通讯作者: Vuister GW

Structure calculation, refinement and validation using CcpNmr Analysis.

• DOI: 10.1107/s1399004714026662
• 发表时间: 2015-01-01
• 期刊: Acta crystallographica. Section D, Biological crystallography
• 作者: Skinner SP;Goult BT;Fogh RH;Boucher W;Stevens TJ;Laue ED;Vuister GW
• 通讯作者: Vuister GW

A software framework for analysing solid-state MAS NMR data.

用于分析固态MAS NMR数据的软件框架。

• DOI: 10.1007/s10858-011-9569-2
• 发表时间: 2011-12
• 期刊: Journal of biomolecular NMR
• 影响因子: 2.7
• 作者: Stevens TJ;Fogh RH;Boucher W;Higman VA;Eisenmenger F;Bardiaux B;van Rossum BJ;Oschkinat H;Laue ED
• 通讯作者: Laue ED