US-UK partnership in NMR structure validation

Lead Research Organisation: University of Leicester
Department Name: Biochemistry

Abstract

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Publications

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Montelione GT (2013) Recommendations of the wwPDB NMR Validation Task Force. in Structure (London, England : 1993)

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Vuister GW (2014) An overview of tools for the validation of protein NMR structures. in Journal of biomolecular NMR

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Ragan TJ (2015) Analysis of the structural quality of the CASD-NMR 2013 entries. in Journal of biomolecular NMR

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Gutmanas A (2015) NMR Exchange Format: a unified and open standard for representation of NMR restraint data. in Nature structural & molecular biology

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Rosato A (2015) The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013. in Journal of biomolecular NMR

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Skinner SP (2016) CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis. in Journal of biomolecular NMR

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Berman H (2019) Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures in Structure

 
Description Prof. Vuister co-organised with the EBI, Hinxton, a workshop to discuss the exchange of data between NMR software packages. The participants included the US partner in this project, Prof. Guy Montelione, and all relevant stakeholders in the field of Biomolecular NMR. A white-paper detailing the issues was first produced in anticipation of the meeting by Prof. Vuister and Dr. Fogh. During the meeting an agreement was reached regarding an NMR exchange format (NEF) that will bridge all the relevant NMR software packages. Importantly, all the participants committed to the ambitious goal of having their software being able to both read and write files compliant with the new format. Consequently, a time scheme for definition of the NEF and implementation was agreed upon during the meeting.
We organized a workshop for PhD students (7/2015, Buxton, UK), as satellite of the CCPN conference, on NMR data management reporting on the new wwPDB NMR-VTF reports and the NEF .
A workshop in Osaka, Japan, (8/2016) again featured a working session on the NEF standard, discussing its official adoption by the wwPDB consortium and a meeting of the NMR-VTF focusing on additional data, sparse data and hybrid methods and formal acceptance of the wwPDB NMR reports. The workshop defined several action points for a follow-up mid 2017. The workgroup met again in Newry (Maine) as satellite meeting to the Gordon conference on computational NMR. A further outreach was done during the 2017 CCPN conference in Stirling.
Exploitation Route A working group was established to produce the initial specifications, to set up a testing framework, to implement software components and to address the issue of long-term management. The working group consists of: Geerten Vuister (chair, University of Leicester), Peter Güntert (University of Frankfurt), Michael Nilges (Institute Pasteur, Paris), Torsten Herrmann (University of Lyon), David Case (Rutger University, Piscataway), Charles Schwieters (NIH, Bethesda), Eldon Ulrich (University of Madison-Wisconsin), Rasmus Fogh (University of Leicester), John Westbrook (RCSB, Piscataway), and Aleksandras Gutmanas (EBI, Hinxton).
Sectors Digital/Communication/Information Technologies (including Software),Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
URL https://github.com/NMRExchangeFormat/NEF/
 
Description NMR is a crucial technique for both fundamental and applied research in biomolecular sciences, health, biotechnology and material sciences. Proper NMR data remediation and data anotation is crucial for it to be a source of future knowledge. Enhances the UK's international standing in research and development
First Year Of Impact 2017
Sector Digital/Communication/Information Technologies (including Software),Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic
 
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
 
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/