Award details

CCPN - A collaborative computational project for macromolecular NMR spectroscopy

Reference	BB/E005071/1
Principal Investigator / Supervisor	Professor Ernest Laue
Co-Investigators / Co-Supervisors	Dr Wayne Boucher, Dr Rasmus Fogh
Institution	University of Cambridge
Department	Biochemistry
Funding type	Research
Value (£)	861,455
Status	Completed
Type	Research Grant
Start date	01/10/2006
End date	30/09/2009
Duration	36 months

Abstract

CCPN is a Collaborative Computing Project for the macromolecular NMR community. Its purpose is to create data standards, promote software integration, produce and disseminate software, and organise conferences and workshops. Over the period of this grant, CCPN intends to: 1) Extend and improve the core software platform, 2) Broaden the macromolecular NMR software suite by expanding our NMR analysis program and collaborating with other groups to integrate programs from European NMR software developers, 3) Integrate the NMR software with related biology efforts, and 4) Continue to organise workshops and study weekends for the UK NMR community. We will extend our NMR analysis program into the areas of (semi)automatic assignment, ligand screening, dynamics and conformers/excited states of proteins, and solid state NMR. The CCPN integrated software also needs to encompass more of the popular NMR software packages as well as tools being developed through the EU projects EXTEND-NMR and EU-NMR. In addition, biologists would benefit greatly by having the same degree of software integration extended to other areas such as bioinformatics, protein production, biophysical characterisation, X-ray crystallography and metabolomics. The data modelling work and its associated code generation machinery represent a considerable investment that can be used to cover a much larger scientific area. We propose to continue to improve the core software platform, to collaborate on the development of Laboratory Information Management Systems (LIMS), and to extend our data model to support the new efforts. We will continue to organize meetings. Our popular yearly meeting for the UK NMR community serves to discuss and disseminate the best practice for determination of macromolecular structures by NMR. We shall also continue our series of workshops discussing software integration, standards and new techniques, and organise courses on the use of our NMR and data modeling software.

Summary

CCPN is a Collaborative Computing Project for the study of biological macromolecules and their structure by NMR spectroscopy. CCPN works 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 NMR programs can work together and use each others' results in a seamless fashion. Secondly, we want to make sure that all the 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 working. Since the CCPN started in 2000, we have defined a standard way of describing scientific data in our particular area. To make it easier to write programs that read and write data in this standard form, we have developed large program libraries for this purpose. 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 the data standard and its program libraries, and we have arranged workshops and annual conferences. In this new application we wish to expand the work we have begun to cover a wider area and to make it useful for more people. The data standard needs to have more program libraries, so that it can also be used by people who want to work in programming languages like C, C++ or Perl. It also has to work better with databases and with very large projects that generate lots of data every day. The data standard should be expanded to cover newer NMR methods, NMR data-processing, structure determination by X-ray crystallography, and other ways of analysing proteins. Our NMR analysis program should be expanded to cover the additional NMR disciplines, moretasks and different ways of working. We will use the results to work with other groups, making their programs work with the data standard. We have contacted many groups that write programs for NMR spectroscopy, and we hope that eventually many of the programs that people use in NMR spectroscopy will work together using the CCPN data standard. We are also talking to groups that work in related areas of biophysics - bioinformatics, protein target selection, large-scale production of proteins, biophysical analysis of proteins, large-scale structure determination, metabolite analysis, drug candidate screening, and analysis of the huge amounts of data all this generates - and we work to make sure that the programs that are used in NMR spectroscopy and in related areas of biophysics can all talk to each other.

Committee	Closed Committee - Biomolecular Sciences (BMS)
Research Topics	Structural Biology, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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