Protein Data Bank in Europe : BBSRC Funding

We have two funding grants from BBSRC. The BBSRC support the CCP4 and CCPN projects with which the PDBe are closely associated.

An E-Science Resource for High Throughput Protein Crystallography

The BBSRC funds a position in the PDBe group in collaboration with University College, London to develop the database replication techniques required to support remote versions of the PDBe database as detailed below....

Lead Partner CLRC Daresbury Laboratory

This proposal addresses an urgent need to develop an end user environment to take advantage of the rapid development of high throughput facilities associated with protein crystallography (HTPX). We are proposing an e-science initiative that will allow the HTPX facilities to be accessed remotely in a fully integrated manner. GRID portals will be developed for each stage. The partners in this application will develop procedures to access all resources, from protein production through to deposition of final refined model. Automatic and user controlled pipelining of data between these stages will be developed, together with software for automatic collection of diffraction data and for exploiting parallel processors for rapid data analysis.

Objectives

To implement an easy-to-use resource for protein crystallography structure determination. The aim is to provide facilities so that a user can access all the required facilities, from target selection to structure deposition, in an easy to use manner from a desktop computer at the home laboratory. The developments will be made initially on the facilities associated with the SRS at Daresbury Laboratory, BM14 at the ESRF. the existing CCP4 project, e-science infrastructure, European Bio-informatics Institute and the Oxford protein production facility. The developments in this proposal, if funded, will be implemented on the SRS and the UK-funded BM14 at the ESRF. They will also be transferrable to the new UK synchrotron, Diamond. It is proposed to carry out these developments in a manner that can, where relevant, be also applied to structural biology in general. Specific objectives are:

• to develop a graphical application interface allowing users to easily interact with all
      the required resources for protein crystallography
  
  
• to implement Grid based portals for protein crystallography, enabling all necessary
      facilities to be available over the internet
  
  
• to implement the infrastructure for automatically pipelining data from the protein production
      to the structural investigations
  
  
• to develop system for controlling the diffraction data collection and analysis based on rules
      as currently used by experts in the field of protein crystallography
  
  
• to implement structure determination software on high-performance computing facilities so
      that rapid feedback can be provided on the success, or otherwise, of the diffraction data
      collection
  
  
• to develop data deposition software to integrate with other software tools in the project as
      automatically as possible and link more broadly with laboratory information systems for
      post genomic structural biology