Award details

CCPN - A Collaborative computational project for macromolecular NMR spectroscopy

Reference	BB/H004130/1
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 (£)	927,787
Status	Completed
Type	Research Grant
Start date	01/10/2009
End date	30/09/2012
Duration	36 months

Abstract

The 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 next three years we intend to: 1) Provide a program to process raw NMR data that is integrated with the CCPN data standard, and which can be used to process NMR data in different ways and be easily modified in the future. 2) Collaborate with other groups to expand support for the analysis of further types of NMR data. 3) Combine computer programs that support the CCPN data standard into a closely integrated pipeline, and work towards automated structure determination starting from raw NMR data. 4) Continue to support our existing users, improve our documentation and maintain the large body of code we have already written. 5) Continue to organise workshops and study weekends for the NMR community. We shall add support for relaxation analysis, reduced dipolar couplings, and solid state NMR. By adding support for small molecule screening and fast structure determination of protein-ligand complexes we hope to make our software more attractive to the pharmaceutical industry. The software will be easy to install, and designed to work either on a Users' own computer or to make use of remote web services. We aim to make NMR more accessible to non-specialists, e.g. by developing a pilot software pipeline that can be used to determine structures directly from raw NMR data. We shall continue to support our users, fix problems, improve documentation, and disseminate our programs through courses and workshops. We plan to make a special effort to improve tools and documentation for programmers, and to spread expertise in using our code to other groups. We will continue to organize meetings, notably our popular annual meetings for the NMR community to discuss and disseminate the best practice for studies of macromolecules using NMR.

Summary

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.

Committee	Research Committee C (Genes, development and STEM approaches to biology)
Research Topics	Structural Biology, Technology and Methods Development
Research Priority	Technology Development for the Biosciences
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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