The Collaborative Computational Project for NMR (CCPN): data analysis, integration and partnerships for NMR in the biosciences
Lead Research Organisation:
University of Leicester
Department Name: Biochemistry
Abstract
The Collaborative Computing Project for NMR (CCPN) was started in 2000 to improve the interoperability of software for biomolecular Nuclear Magnetic Resonance (NMR), and to promote a collaborative community for software users and programmers. Over the past fifteen years, the project has produced the CcpNmr suite of software for interactive NMR data analysis and software integration, which 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, thus helping to maximise the impact of biological NMR research. CCPN has a leading role in the development of a NMR data-exchange format and coordination of NMR instrumentation proposals for RCUK and BIS.
With the current proposal we seek to continue the CCPN project and to further expand its user community. Hence, over the next grant period we aim to:
1. Maintain and expand the CCPN code base.
2. Expand the capabilities and versatility of the CCPN software package.
3. Facilitate NMR-based scientific developments in collaboration with the partners of the project and the NMR community at large.
4. Promote and expand user uptake and user development of the software.
5. Provide support for research data management (RDM).
6. Support the training of researchers, sharing of knowledge and exchange of best-practices by the UK and international NMR community.
With the current proposal we seek to continue the CCPN project and to further expand its user community. Hence, over the next grant period we aim to:
1. Maintain and expand the CCPN code base.
2. Expand the capabilities and versatility of the CCPN software package.
3. Facilitate NMR-based scientific developments in collaboration with the partners of the project and the NMR community at large.
4. Promote and expand user uptake and user development of the software.
5. Provide support for research data management (RDM).
6. Support the training of researchers, sharing of knowledge and exchange of best-practices by the UK and international NMR community.
Technical Summary
Version-3 of the CcpNmr suite has led to new, user-friendly applications with four different components: AnalysisAssign, AnalysisStructure, AnalysisMetabolomics and AnalysisScreen, which each cover different aspects of biomolecular NMR. The programs use a new, modern intuitive graphical interface with drag-and-drop. We will ensure that current and newly developed software components will continue to be easy to use, fully documented and thoroughly tested, with dedicated modules for specialised 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, metabolomics and small molecule screening.
To promote CCPN and increase user uptake, together with our partners we will embed CCPN in a broad range of scientific projects, enhancing its impact in the structural biological community. The greatly enhanced flexibility of the code will promote dedicated program adaptation to the working procedures of individual laboratories. We plan to use the modular capabilities of version-3 and the reorganised library of high-level utility functions to allow for more groups to start writing software for their own specific practices. CCPN will also foster its collaborations with industry. The CCPN software will be extensively demonstrated through workshops and documentation.
CCPN will continue its crucial role as intermediary between the UK and international NMR community, by fostering contacts with the national NMR facilities, MRC-Francis Crick Institute, HWB-NMR, and Warwick solid-state NMR facility, other CCPs, the international WeNMR, CASD-NMR and NEF efforts.
To strengthen the UK NMR community, we will continue the successful series of UK CCPN conferences and teaching programs for all researchers. We will also continue the comprehensive help and support for CCPN users, participate in international efforts in knowledge sharing and exchange of best practices, and engage in training and teaching through workshops, papers and (video) tutorials.
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.
To promote CCPN and increase user uptake, together with our partners we will embed CCPN in a broad range of scientific projects, enhancing its impact in the structural biological community. The greatly enhanced flexibility of the code will promote dedicated program adaptation to the working procedures of individual laboratories. We plan to use the modular capabilities of version-3 and the reorganised library of high-level utility functions to allow for more groups to start writing software for their own specific practices. CCPN will also foster its collaborations with industry. The CCPN software will be extensively demonstrated through workshops and documentation.
CCPN will continue its crucial role as intermediary between the UK and international NMR community, by fostering contacts with the national NMR facilities, MRC-Francis Crick Institute, HWB-NMR, and Warwick solid-state NMR facility, other CCPs, the international WeNMR, CASD-NMR and NEF efforts.
To strengthen the UK NMR community, we will continue the successful series of UK CCPN conferences and teaching programs for all researchers. We will also continue the comprehensive help and support for CCPN users, participate in international efforts in knowledge sharing and exchange of best practices, and engage in training and teaching through workshops, papers and (video) tutorials.
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.
Planned Impact
The CCPN project constitutes a long-standing, highly-regarded, advanced technological software development and community-building project. Its continued development and maintenance is crucial, for the field of NMR spectroscopy itself, because it is the only fully capable and up-to-date NMR analysis platform, and also for the larger scientific and societal context as a result of CCPN's role in the development of international standards for data deposition and remediation. Thus, CCPN serves as an example of the acknowledged imperative for the UK to be a leader in the global knowledge economy.
The impact extends to a number of areas:
1. Supporting academic research excellence. The CCPN software package is essential for the research of a large number of UK and worldwide NMR scientists active in the biomedical sciences, including many MRC-funded PIs. Continuing support, improvement and expansion of the software with the latest state-of-the-art tools is essential, as the improved tools developed by CCPN and its partners drives their biomedical NMR-based research programs and stimulate the developments in data-centred science and -omics type research.
2. Support for industrial innovation and research capacity. Both drug discovery and metabolomics require the development of dedicated software tools. By developing an open-source, readily customisable software platform, CCPN supports industrial innovation, in particular for small- and medium- sized companies that alone cannot afford the development of the technologically demanding NMR technique. The continuing industrial support of CCPN underscores this notion.
3. Providing a scientifically well-trained professional workforce. The presence of a well-educated and technologically skilled workforce is crucial for societal development. CCPN provides direct training for graduate students and post-docs who will soon contribute to the core of the UK technological workforce. By interacting with CCPN at conferences and workshops and by using its technological base, they are trained in scientific thinking, problem solving and scientific software development. These skills are widely applicable and are useful well beyond the specific problems where they were first applied.
4. Driving technological developments that benefit the UK population through improved health-care. NMR has emerged as a crucial tool in the quest for dedicated, personalised medicine approaches. Not only does NMR contribute to our understanding of the structure and interactions of biomolecules in a variety of states (folded, aggregated, unfolded), NMR-assisted drug discovery has also proved to be one of the leading components in the search for new therapeutic agents, not least in methods for fragment-based lead compound identification. Metabolomics presents a second area of technological development of great potential benefit to the general UK public. Accurate, detailed and timely detection of disease is nearly always beneficial for effective treatment and improves the chances of recovery. NMR has emerged as an excellent tool for the analysis of body fluids and for the attempts to elucidate relevant biomarkers. Specific metabolite patterns are starting to be recognised and correlated with specific disease states. Thus, NMR provides for a great potential as diagnostic tool that will benefit the society at large.
5. Education of the general public. Current high-school students present the future generation of potential scientists. The NMR technique is part of the GCE A- level chemistry curriculum. The self-contained nature of the CCPN software tools and their dedicated provisions for 1D data, provide for an excellent way to familiarise the students with the curriculum objectives. By providing actual NMR data together with suitable tools, tutorial videos and hands-on approaches, the students' imagination will be aroused.
The impact extends to a number of areas:
1. Supporting academic research excellence. The CCPN software package is essential for the research of a large number of UK and worldwide NMR scientists active in the biomedical sciences, including many MRC-funded PIs. Continuing support, improvement and expansion of the software with the latest state-of-the-art tools is essential, as the improved tools developed by CCPN and its partners drives their biomedical NMR-based research programs and stimulate the developments in data-centred science and -omics type research.
2. Support for industrial innovation and research capacity. Both drug discovery and metabolomics require the development of dedicated software tools. By developing an open-source, readily customisable software platform, CCPN supports industrial innovation, in particular for small- and medium- sized companies that alone cannot afford the development of the technologically demanding NMR technique. The continuing industrial support of CCPN underscores this notion.
3. Providing a scientifically well-trained professional workforce. The presence of a well-educated and technologically skilled workforce is crucial for societal development. CCPN provides direct training for graduate students and post-docs who will soon contribute to the core of the UK technological workforce. By interacting with CCPN at conferences and workshops and by using its technological base, they are trained in scientific thinking, problem solving and scientific software development. These skills are widely applicable and are useful well beyond the specific problems where they were first applied.
4. Driving technological developments that benefit the UK population through improved health-care. NMR has emerged as a crucial tool in the quest for dedicated, personalised medicine approaches. Not only does NMR contribute to our understanding of the structure and interactions of biomolecules in a variety of states (folded, aggregated, unfolded), NMR-assisted drug discovery has also proved to be one of the leading components in the search for new therapeutic agents, not least in methods for fragment-based lead compound identification. Metabolomics presents a second area of technological development of great potential benefit to the general UK public. Accurate, detailed and timely detection of disease is nearly always beneficial for effective treatment and improves the chances of recovery. NMR has emerged as an excellent tool for the analysis of body fluids and for the attempts to elucidate relevant biomarkers. Specific metabolite patterns are starting to be recognised and correlated with specific disease states. Thus, NMR provides for a great potential as diagnostic tool that will benefit the society at large.
5. Education of the general public. Current high-school students present the future generation of potential scientists. The NMR technique is part of the GCE A- level chemistry curriculum. The self-contained nature of the CCPN software tools and their dedicated provisions for 1D data, provide for an excellent way to familiarise the students with the curriculum objectives. By providing actual NMR data together with suitable tools, tutorial videos and hands-on approaches, the students' imagination will be aroused.
Publications
Bate N
(2018)
A Novel Mechanism for Calmodulin-Dependent Inactivation of Transient Receptor Potential Vanilloid 6.
in Biochemistry
Berman HM
(2019)
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
in Structure (London, England : 1993)
Bokhovchuk FM
(2018)
The Structural Basis of Calcium-Dependent Inactivation of the Transient Receptor Potential Vanilloid 5 Channel.
in Biochemistry
Chandru A
(2018)
Sin3A recruits Tet1 to the PAH1 domain via a highly conserved Sin3-Interaction Domain.
in Scientific reports
Hommel U
(2023)
Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1ß.
in Nature communications
Lescanne M
(2017)
Methyl group assignment using pseudocontact shifts with PARAssign.
in Journal of biomolecular NMR
Mureddu L
(2019)
Simple high-resolution NMR spectroscopy as a tool in molecular biology.
in The FEBS journal
Mureddu LG
(2022)
Fragment-Based Drug Discovery by NMR. Where Are the Successes and Where can It Be Improved?
in Frontiers in molecular biosciences
Mureddu LG
(2020)
CcpNmr AnalysisScreen, a new software programme with dedicated automated analysis tools for fragment-based drug discovery by NMR.
in Journal of biomolecular NMR
Description | CCPN CYANA integration |
Organisation | ETH Zurich |
Country | Switzerland |
Sector | Academic/University |
PI Contribution | Jointly developed the CCPN CYANA importer. CCPN implemented the required software on the basis of specification of needs of the partner. |
Collaborator Contribution | Meier's group provided specification, test data and did the testing. |
Impact | Incorporation of the software tool in the CcpNmr Analysis 2.4 release |
Start Year | 2013 |
Description | CCPN-Farseer integration |
Organisation | University of Barcelona |
Country | Spain |
Sector | Academic/University |
PI Contribution | The tremendous improvement in efficiency that has obtained by the method developped by the Farseer team, prompted our partner and us to share the tool with the broad NMR community. For that, we are now implementing Farseer in the CCPNMRv3 project. We (i.e. CCPN) have already developed the basic, yet functional plugin allowing the Farseer team to further customise their tool within the CcpNmr Analysis version-3 framework. |
Collaborator Contribution | The analysis of the NMR spectra ultimately concludes with the generation of peaklists which are none other than text files in our computer hard disk - peaklists contain all the information encoded in the NMR spectra (peak assignments, peak position, height, volume, etc). Scientific projects that rely on NMR to solve biologically relevant problems mainly require the comparison of peaklists from different samples and experimental conditions which translates in restraints calculation and final data plotting; for example, in protein-protein or protein-ligand interactions, domain dynamics, or usage of paramagnetic NMR restraints. Before a peaklist can be used reliably, it needs to be treated according to the projects specifications. The treatment of the peaklist files is traditionally carried out manually by the researcher in spreadsheet documents. Handling peaklists manually is very time consuming and, above all, opens the door to human-prone mistakes. Moreover, obtaining a reliable peaklist often requires an interactive process of analysis and correction, which increases task repetition and time consumption. Additionally, when several projects run in parallel in a laboratory, there is a strong demand for fast, yet reliable, NMR peaklist analysis, data treatment and plotting, so that experimental conclusions can be drawn quickly. The necessity to cope with such issues and demands led us to develop a Python3-based tool that instantly treats peaklists, calculates all the required parameters/restraints and plots the obtained data into analysable results. Our aim is to automatize this heavy, repetitive and dangerous tasks of manually treating, analysing and plotting NMR peaklists derived data; thus, reducing the time consumed from hours/days/weeks to few minutes and avoiding the introduction of mistakes. By now, the most common NMR related tasks in peaklist treatment, parameter calculation and plotting have been implemented. Specifically, analysis of titrations in protein-protein/ligand interactions, representation and analysis of paramagnetic relaxation enhancements (PRE) data and chemical shift perturbation data. We have also prepared a set of plotting templates that can represent the obtained data with clarity and with publication quality; indeed, our most recent publications already present plots generated this way[1,2,3] - from peaklists to publication in one click! To us, the most outstanding characteristic of Farseer is that it allows the analysis and representation of titration/comparison data up to three experimental conditions; which means that a cubic matrix of, for example, 60 related peaklists can be analyzed and correlated simultaneously, generating large amounts of data automatically. |
Impact | The collaboration has served as the nucleus for fruther engagement, e.g. as a iNext proposal. |
Start Year | 2016 |
Description | NMRbox consultation |
Organisation | University of Connecticut |
Country | United States |
Sector | Academic/University |
PI Contribution | NMRbox is a resource for biomolecular NMR (Nuclear Magnetic Resonance) software. It provides tools for finding the software you need, documentation and tutorials for getting the most out of the software, and cloud-based virtual machines for executing the software. |
Collaborator Contribution | We collaborate on all issues regarding software development, outreach and technology sharing. |
Impact | Partner in CCPN continuation grant application |
Start Year | 2019 |
Description | Novartis (partnership collaboration) |
Organisation | Novartis |
Department | Novartis Institutes for BioMedical Research Switzerland |
Country | Switzerland |
Sector | Private |
PI Contribution | We are currently engaging in a joint project to apply our tools and software expertise in NMR-based drug discovery to projects of direct interest to Novartis. We have regular project meetings to exchange knowledge and ideas and train their staff in the usage of the CcpNmr Analysis software platform for advanced NMR data analysis. Proper translational research and the access to state-of-the-art technologies by pharmaceutical industry is key to maintaining and reinforcing an advanced technological industrial base and reinforces the UK desire to be at the forefront of biomedical research. |
Collaborator Contribution | License fees, in-kind contributions, data, expertise |
Impact | Drug-discovery, Structural-Biology, software-development, data-management. |
Start Year | 2020 |
Description | connectNMR 2019 |
Organisation | University of Liverpool |
Department | School of Life Sciences Liverpool |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | A newly emerged effort to coordinate NMR activities across the UK, to promote sharing, knowledge exchange, and access to NMR research infrastructure equipment. |
Collaborator Contribution | We constitute one of the funded sides and as CCPN function as a key partner in the effort. |
Impact | NA |
Start Year | 2018 |
Title | CcpNmr Analysis version 2.5.0 |
Description | Legacy programme; new windows version released. |
Type Of Technology | Software |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | Used in >300 laboratories worldwide |
URL | https://www.ccpn.ac.uk/ |
Title | CcpNmr AnalysisAssign beta2 |
Description | CcpNmr AnalysisAssign beta2 |
Type Of Technology | Software |
Year Produced | 2017 |
Impact | Updated and improved version |
Title | CcpNmr AnalysisAssign version 3 beta1 release |
Description | We released CcpNmr AnalysisAssign version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. We include workflow for backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations. |
Type Of Technology | Software |
Year Produced | 2016 |
Open Source License? | Yes |
Impact | This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. |
URL | http://www.ccpn.ac.uk/v3-software |
Title | CcpNmr AnalysisAssign version 3.0-beta3, beta4 |
Description | CcpNmr AnalysisAssign beta3 and beta4 for NMR data analysis and visualisation. |
Type Of Technology | Software |
Year Produced | 2018 |
Impact | Updated and improved versions; Part of the development scheme with enhanced performance and functionality. |
Title | CcpNmr AnalysisAssign version 3.0.4 |
Description | Premier software package with unique capabilities for liquid-state and solid-state NMR data analysis.New releases for Mac OSX, Linux and Windows. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2200 times. |
URL | https://ccpn.ac.uk |
Title | CcpNmr AnalysisAssign, release 3.1.0 |
Description | Premier NMR software package with unique capabilities for liquid-state and solid-state NMR data analysis. New releases for Mac OSX, Linux and Windows. |
Type Of Technology | Software |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2300 times. CcpNmr programme suite now used by 23 bioPharma companies. |
Title | CcpNmr AnalysisAssign, releases 3.0-beta5 and 3.0.0 |
Description | Premier software package with unique capabilities for liquid-state and solid-state NMR data analysis. |
Type Of Technology | Software |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2100 times. Used by four industrial subscribers, with two pending. |
URL | https://www.ccpn.ac.uk |
Title | CcpNmr AnalysisAssign, releases 3.0.0, 3.0.1 and 3.0.2 |
Description | Premier software package with unique capabilities for liquid-state and solid-state NMR data analysis. |
Type Of Technology | Software |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2200 times. Used by seven industrial subscribers, with four pending |
URL | https://www.ccpn.ac.uk/ |
Title | CcpNmr AnalysisAssign, releases 3.0.3 |
Description | Premier software package with unique capabilities for liquid-state and solid-state NMR data analysis.New releases for Mac OSX, Linux and Windows. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2200 times. |
URL | https://ccpn.ac.uk |
Title | CcpNmr AnalysisMetabolomics version 3.0-alfa1 |
Description | CcpNmr AnalysisMetabolomics alfa1 for NMR metabolomics data analysis and visualisation. |
Type Of Technology | Software |
Year Produced | 2018 |
Impact | N/A |
Title | CcpNmr AnalysisMetabolomics, release 3.0-beta1 |
Description | Premier software package with unique capabilities for NMR-based metabolomics data analysis. |
Type Of Technology | Software |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2100 times. Used by four industrial subscribers, with two pending |
URL | https://www.ccpn.ac.uk/ |
Title | CcpNmr AnalysisMetabolomics, releases 3.0.3 and 3.0.4 |
Description | Premier software package with unique capabilities for liquid-state and solid-state NMR data analysis with a focus on NMR metabolomics. New releases for Mac OSX, Linux and Windows. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2200 times |
URL | https://ccpn.ac.uk |
Title | CcpNmr AnalysisScreen alfa |
Description | First release CcpNmr AnalysisScreen; a dedicated programme for the analysis of NMR screening data |
Type Of Technology | Software |
Year Produced | 2017 |
Impact | NA |
Title | CcpNmr AnalysisScreen versions 3.0-beta1, beta2 (2018) |
Description | Beta1 and Beta2 releases of AnalysisScreen; a dedicated programme for the analysis of NMR screening data |
Type Of Technology | Software |
Year Produced | 2018 |
Impact | The programme was used for a thorough and systematic analysis of NMR-based screening protocols. Papers describing the programme and this analysis are currently ion preparation. |
Title | CcpNmr AnalysisScreen, release 3.0-beta2 |
Description | Premier software package with unique capabilities for NMR-based screening data analysis. |
Type Of Technology | Software |
Year Produced | 2019 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2100 times. Used by four industrial subscribers, with two pending. |
URL | https://www.ccpn.ac.uk |
Title | CcpNmr AnalysisScreen, release 3.1.0 |
Description | Premier NMR software package with unique capabilities for NMR-based fragment-based drug discovery. New releases for Mac OSX, Linux and Windows. |
Type Of Technology | Software |
Year Produced | 2022 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2300 times. CcpNmr programme suite now used by 23 bioPharma companies. |
Title | CcpNmr AnalysisScreen, releases 3.0.0, 3.0.1 and 3.0.2 |
Description | Premier biomolecular NMR software package with unique capabilities for NMR-based screening data analysis. |
Type Of Technology | Software |
Year Produced | 2020 |
Open Source License? | Yes |
Impact | Used by seven industrial subscribers, with four pending. |
URL | https://www.ccpn.ac.uk/ |
Title | CcpNmr AnalysisScreen, releases 3.0.3 and 3.0.4 |
Description | Premier software package with unique capabilities for liquid-state and solid-state NMR data analysis with a focus on NMR-base small molecule screening. New releases for Mac OSX, Linux and Windows. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2200 times. |
URL | https://ccpn.ac.uk |
Title | CcpNmr AnalysisStructure, release 3.0.4 |
Description | remier software package with unique capabilities for liquid-state and solid-state NMR data analysis with a focus on NMR structure generation and validation. New releases for Mac OSX, Linux and Windows. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | All CcpNmr packages jointly cited >2200 times. |
URL | https://ccpn.ac.uk |
Title | CcpNmr ChemBuild version 1.0 |
Description | ChemBuild is a program to generate, modify and convert molecular topology descriptions used for (bio)molecular simulations. It allows the users to adjust the templates in an interactive fashion. |
Type Of Technology | Software |
Year Produced | 2016 |
Open Source License? | Yes |
Impact | Enhances the UK's international standing in research and development. |
URL | http://www.ccpn.ac.uk/v3-software |
Title | The NMR Exchange Format (NEF) |
Description | The NMR Exchange Format (NEF) has been developed in a collaboration between the CCPN, the BioMagResBank, the RCSB, and the main developers of macromolecular NMR software (Peter Guntert (CYANA), Charles Schwieters (XPLOR-NIH), Michael Nilges (ARIA), Torsten Herrmann (UNIO), David Wishart, David Case (AMBER), Guy Montelione (AutoAssign, ASDP)). It covers sequence, chemical shifts, spectra, peak lists, and restraints. The format specification is controlled by consensus of the partners, and all developers have committed to supporting the format as an input/output exchange format. Version 1.0 of the format specification is now stable and fully supported by CCPN, and will be supported by the upcoming release of NMR-STAR (version 3.2.0.1). |
Type Of Technology | Software |
Year Produced | 2017 |
Open Source License? | Yes |
Impact | For over 20 years, efforts to establish seamless NMR data exchange between different programs have failed, relying on conversion between a variety of formats instead with a concomitant risk of information loss or misinterpretation. Efforts to develop universal NMR data converters have been challenged because some formats omit information required by other formats, and full parsing of each software-specific format has proven to be impossible. The current situation hampers the proper archiving and use of biomolecular NMR data, and prevents the routine inclusion of NMR restraint validation in the wwPDB NMR validation pipeline. The new NMR exchange format was developed in close consultation and with support of developers of key software packages used for NMR structure determination and refinement, with the aim of attaining a unified approach to represent NMR restraints and associated data. Together, they agreed on and successfully implemented and tested an NMR data representation and devised a governance structure for its maintenance and further development. The authors of fourteen different packages already committed during the initial discussions, with new ones joining the efforts since. |
URL | https://github.com/NMRExchangeFormat/NEF/ |