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The Collaborative Computational Project for NMR (CCPN): Supporting biomolecular NMR and community driven NMR software development.

NMR 协作计算项目 (CCPN)：支持生物分子 NMR 和社区驱动的 NMR 软件开发。

基本信息

批准号：
MR/L000555/1
负责人：
Geerten Vuister
金额：
$ 96.22万
依托单位：
University of Leicester
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2013
资助国家：
英国
起止时间：
2013 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=MR%2FL000555%2F1
关键词：
Collaborative Computational Project NMR CCPN

项目摘要

The Collaborative Computing Project for NMR (CCPN) was started in 2000 to improve the interoperability of software for biomolecular NMR and to promote a collaborative community of software users and programmers. Over the past twelve years, the project has produced the CcpNmr suite of software for interactive NMR data analysis and integration and the CCPN data standard for macromolecular NMR. The software is now used worldwide by >1000 users. Through its conferences and workshops, CCPN also promotes best practices in both computational and experimental aspects of NMR.With this proposal we seek to continue and further expand the CCPN project and its user community. Building upon the CCPN software platform, new and emerging aspects of NMR and integrative structural biology techniques will now be targeted. For the current period, we aim to:1. Develop a fully implemented version 3 (v3) of the CCPN software package.2. Promote and expand the user uptake and user development of the software.3. Facilitate the use and sharing of state-of-the-art NMR software technology. 4. Strengthen the training of people, sharing of knowledge and exchange of best-practice's by the UK NMR community.Version 3 of the CcpNmr suite has led to new, user-friendly applications like SpecView and ChemBuild. These are the first CCPN programs to use an entirely new graphical system based on the modern, multi-platform Qt libraries. During the new period, we will bring the same approach to the Analysis and FormatExchange programs. We will ensure that v3 components are easy to use, fully documented and thoroughly tested, with dedicated modules for specialized tasks and means to interact with external programs and services. This will provide flexible tools to support scientific collaborations and advance important areas such as solid state NMR, small molecule screening and metabolomics.To promote CCPN and increase user uptake, together with our partners we will embed CCPN in a broader range of scientific projects, enhancing its impact in the structural biological community. The greatly enhanced flexibility of the new code will promote dedicated program adaptation to the working procedures of individual laboratories. We plan to use the modular capabilities of CcpNmr v3 and a reorganised library of high-level utility functions to allow for more groups to start writing software for their own specific practices. To ease user uptake a dedicated Analysis Lite, optimized for simplicity rather than for complex problems, will be developed. The CCPN software will be extensively demonstrated through workshops and documentation.Together with its partners, CCPN will continue the process of software development and integration by means of direct integration of available methods or by using web-based services developed by third parties. Thus, CCPN users will have easy access to a software pipeline for biological NMR, which allows them to proceed smoothly from spectral data via resonance assignment to structure generation and database deposition. CCPN will collaborate with CCISB groups at Harwell to allow NMR to fulfill its role in biophysics and integrated science.To strengthen the UK NMR community, we will continue the successful series of UK CCPN conferences and teaching programs for (young) researchers. We will also continue the comprehensive help and support for CCPN users and participate in international efforts in knowledge sharing and exchange of best practices by efforts such as WeNMR. We will closely confer with the NMR facilities in Mill Hill, Birmingham and Warwick.Oversight of the project will be maintained by the CCPN Executive Committee, with representative members from the UK NMR community and CCPN's international Scientific Advisory Board.

核磁共振协同计算项目（CCPN）于2000年启动，旨在提高生物分子核磁共振软件的互操作性，并促进软件用户和程序员之间的协作社区。在过去的12年里，该项目已经生产了用于交互式核磁共振数据分析和集成的CCPN软件套件和用于大分子核磁共振的CCPN数据标准。该软件目前在世界范围内被bb101000名用户使用。通过其会议和研讨会，CCPN还促进核磁共振计算和实验方面的最佳实践。通过此提案，我们寻求继续并进一步扩展CCPN项目及其用户社区。建立在CCPN软件平台上，新的和新兴的核磁共振和综合结构生物学技术方面现在将是目标。在当前阶段，我们的目标是：1。开发一个完全实现的CCPN软件包的第3版（v3）。促进和扩大用户对软件的吸收和用户开发。促进最先进的核磁共振软件技术的使用和共享。4. 加强人员培训、知识分享和英国核磁共振社区最佳实践的交流。CcpNmr套件的第3版带来了新的、用户友好的应用程序，如SpecView和ChemBuild。这是第一个使用基于现代多平台Qt库的全新图形系统的CCPN程序。在新的阶段，我们将把同样的方法引入到Analysis和FormatExchange程序中。我们将确保v3组件易于使用，有完整的文档和彻底的测试，有专门的模块用于专门的任务和与外部程序和服务交互的手段。这将为支持科学合作和推进固态核磁共振、小分子筛选和代谢组学等重要领域提供灵活的工具。为了促进CCPN并增加用户的使用，我们将与合作伙伴一起将CCPN嵌入到更广泛的科学项目中，增强其在结构生物群落中的影响。新规范的灵活性大大增强，将促进专门的程序适应个别实验室的工作程序。我们计划使用CcpNmr v3的模块化功能和重组的高级实用函数库，以允许更多的团队开始为他们自己的特定实践编写软件。为了方便用户使用，将开发一个专门的Analysis Lite，为简单而不是复杂的问题进行优化。CCPN软件将通过研讨会和文件进行广泛的演示。CCPN将与其合作伙伴一起，通过直接集成可用方法或使用第三方开发的基于web的服务，继续进行软件开发和集成过程。因此，CCPN用户可以很容易地访问生物核磁共振的软件管道，这使他们能够顺利地从光谱数据通过共振分配到结构生成和数据库沉积。CCPN将与哈维尔的CCISB小组合作，使NMR在生物物理学和综合科学中发挥其作用。为了加强英国核磁共振社区，我们将继续为（年轻）研究人员成功举办一系列英国CCPN会议和教学计划。我们亦会继续为CCPN使用者提供全面的协助和支援，并透过WeNMR等机制，参与国际间的知识分享和最佳实务交流。我们将与米尔希尔、伯明翰和沃里克的核磁共振设施密切磋商。该项目将由CCPN执行委员会负责监督，该委员会的代表成员来自英国核磁共振科学界和CCPN的国际科学顾问委员会。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Sin3A recruits Tet1 to the PAH1 domain via a highly conserved Sin3-Interaction Domain.

DOI：
10.1038/s41598-018-32942-w
发表时间：
2018-10-02
期刊：
Scientific reports
影响因子：
4.6
作者：
Chandru A;Bate N;Vuister GW;Cowley SM
通讯作者：
Cowley SM

Methyl group assignment using pseudocontact shifts with PARAssign.

DOI：
10.1007/s10858-017-0136-3
发表时间：
2017-12
期刊：
Journal of biomolecular NMR
影响因子：
2.7
作者：
Lescanne M;Skinner SP;Blok A;Timmer M;Cerofolini L;Fragai M;Luchinat C;Ubbink M
通讯作者：
Ubbink M

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