Award details

Unified data resource for NMR spectral and PDB data via and enhanced deposition visualisation and validation autodep system development

Reference	BB/E007511/1
Principal Investigator / Supervisor	Professor Gerard Kleywegt
Co-Investigators / Co-Supervisors	Dr Wim Vranken
Institution	EMBL - European Bioinformatics Institute
Department	Protein Data Bank in Europe
Funding type	Research
Value (£)	461,727
Status	Completed
Type	Research Grant
Start date	01/01/2007
End date	31/12/2011
Duration	60 months

Abstract

This proposal has two inter-related aims: (i) Develop an integrated system for the deposition of spectral data and coordinates based on the CCPN data model for NMR, and combined studies, together with a relational database management system. The deposition system will issue both PDB and BMRB database accession codes and in collaboration with the wwPDB partners. (ii) Develop a common access portal to deliver both NMR data and model coordinates with easily accessible visualization tools, annotations, and validation criteria. The first task will be achieved by extending our existing systems. At the EBI deposition to the PDB and EMDB is via the Autodep4 deposition system. These deposition interfaces and servers are metadata driven systems, which prepare entries for loading into the MSD database. The systems are flexible, extendable and easy to maintain and manage. XML based dictionaries drive the deposition interface, which stores data in XML format. Having the data in XML format is extremely beneficial, as this is easy to parse and can be transformed into any other required format like PDB. To provide the NMR community with an access portal, especially for the visualisation of the data archived in the BMRB database, linked to the coordinate data held in the PDB, we will tune the MSD Java viewing system, AstexViewer@MSD-EBI. This system is the result of our work with Astex International to develop an interactive web based viewer with the functionality to display the results from database searches for the MSD services. A major emphasis of the viewer has been the presentation of information associated with the display of multiple superposed structures and sequences that result from a database query. The viewer is ideally suited to be used in the analysis of spectral data with both sequence and coordinates. We will develop modules that will allow macromolecular NMR data to be presented in a number of different views.

Summary

The goal of this proposal is to ensure that NMR investigators in Europe have access to a convenient local system of deposition of NMR structures and all associated data in a manner similar to that developed by the RCSB and BMRB in the United States. We will build on our well-established database systems, and we plan to use our infrastructure by building on top of this for NMR Spectral data deposition and retrieval. We have developed web based Java/XML deposition systems, AutoDep4 for the PDB and the EmDep for EMDB and from this base we will extend these systems to allow for the archival and routing of 3D structure data to both the PDB for coordinate information and to the BMRB for NMR spectral data. In addition as a member of the wwPDB the MSD group is committed to process a greater proportion of PDB submissions as part of the global partnership. NMR data contains a wealth of information about the structure and dynamics of biological macromolecules. It is, however, often difficult to extract this information in a meaningful way. For example, the chemical shift values of certain protein backbone atoms can be directly used to determine the secondary structure of a protein, but because chemical shift values are averaged between all the different conformations a molecule adopts the chemical shifts of more flexible backbone regions or side chain atoms are much harder to interpret. In addition, information about, for example, the width of NMR signals is seldom used in solution NMR. The current deposition system presents a number of major difficulties for both depositors and potential users of NMR spectral data. For most depositors, coordinates and spectral data are deposited semi-independently of one another in order to archive a set of experiments. In particular, the time-consuming process of entering metadata related to the experiment must be performed twice, through two different processes, each of which collects a different subset of the relevant experimental data. For potential users of coordinate data the linkage to NMR spectral data there is no simple display option to view such data over the web. We will also extend the functionality of our visualisation and analysis software for molecular structures, AstexViewer@MSD-EBI, for the display and analysis of NMR data in relation to 3D structure and chemical properties to give a fast, object-based access to complex analyses. By enhancing these existing tools, tuned to specific NMR applications, we will provide powerful applications for the NMR structural community. The MSD database contains NMR information that is directly linked to the structure coordinates of biological macromolecules and opens exciting prospects for being able to relate NMR data to the structures in a more meaningful way. In particular from a structure point of view, the restraints are crucial and to visualise the distribution of restraints in relation to structure will be an important deliverable in this proposal. We will carry out a 'large scale' structure related analysis of the spectral data extracted from the BMRB database combining this with specific MSD data on chemical entities in relation to protein chemical shift data. As more relaxation data, which is directly related to the dynamics of the molecule, becomes available it is crucial that large-scale analyses are performed that incorporates as much data as possible. There will be two major results from this grant. First we will have developed a unified deposition interface for the deposition of all data related to macromolecular structure determination by NMR for both PDB specific data and BMRB specific data. Second we will have developed an access portal for the visualisation and analysis of this data suitable for the NMR community to apply to a wide range of problems.

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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