CCP4 and Computational Biology Groups

The CCP4 and Computational Biology groups of CSED are involved in a number of activities, which are briefly described below. Each area has extensive web pages which give more details. For more information, please contact Dr Martyn Winn These activities cover laboratory procedures (PIMS), experimental structure determination (CCISB, CCP4 and e-HTPX), and simulations of dynamic behaviour (Biomolecular simulation).

Computational Centre for Integrated Structural Biology (CCISB)

CCISB is a newly-established centre that provides computational support to the European community of structural biologists across the full range of disciplines, allowing a single point of access for software and support, and encouraging standardisation between the different disciplines. Research Complex at Harwell The Centre consists of a hub hosted by the Computational Science and Engineering Department of the STFC, and located at the Research Complex at Harwell adjacent to the Diamond synchrotron, together with nodes at Cambridge, York, STFC Daresbury Laboratory and Bristol providing specific expertise. Initial contributing groups include CCP4, CCPN, CCPB, PiMS and Diamond. As the Centre develops, additional software groups from across Europe will be included, either as formal nodes or as recognised collaborators, reflecting the distributed nature of software development.

Biomolecular simulation

Computational Biology is a new theme of the Computational Science and Engineering Department. It builds on considerable biological work done elsewhere in the department, in particular in the Computational Chemistry and CCP4 groups. It also exploits links with experimental groups in STFC.

Initial work has concentrated on the ectodomain of human Epidermal Growth Factor Receptor, modelled at both atomistic and coarse-grained levels.

CCP4

The Collaborative Computational Project Number 4 in Protein Crystallography was set up in 1979 to support collaboration between researchers working on such software in the UK, and to assemble a comprehensive collection of software to satisfy the computational requirements of the relevant UK groups. CCP4 was originally supported by the UK Science and Engineering Research Council (SERC), and is now supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The project is coordinated at STFC Daresbury Laboratory.

The results of this effort gave rise to the CCP4 program suite, which is now distributed to academic and commercial users world-wide. The software covers all stages in the experimental determination of protein structure from the X-ray diffraction images through to the validated structure. The CCP4 project also runs a vigorous educational programme through conferences, workshops, newsletters and tutorials.

PIMS

The PIMS project aims to produce a commercial-quality Laboratory Information Management System (LIMS) to meet the needs of structural biology laboratories. In particular, it covers laboratory procedures used to produce and purify desired proteins. These proteins may in turn be crystallised for use in structure determination via protein crystallography.

The project, funded by the BBSRC-SPoRT initiative for 5 years, is for the incremental development and deployment of a LIMS, initially for use by the other BBSRC-funded SPoRT consortia: SSPF and MPSI, but to be freely available to the scientific community as a whole.

Designed with flexibility in mind, PIMS will be suitable for use in all academic environments ranging from the single, hypothesis driven laboratory to multi-site and automated high-throughput settings.

e-HTPX

e-HTPX (2002-2007) was a BBSRC-funded e-science pilot project. The aim was to unify the procedures of experimental protein structure determination into a single all encompassing interface from which users can initiate, plan, direct and document their experiment either locally or remotely from a desktop machine.

The developments have been built around the facilities associated with the SRS at Daresbury Laboratory, BM14 at the ESRF, the CCP4 project and York University Structural Biology Laboratory, the existing e-science infrastructure, the European Bioinformatics Institute and the Oxford protein production facility. Others involved in specific aspects of the project include Structural Medicine, Cambridge and the Computer Science Department, Cardiff University. This brings together the key UK players in high-throughput protein crystallography (HTPX) and e-science. However, the intention is to develop a comprehensive resource for the whole of the UK and in particular one that is transferable to the new UK synchrotron, Diamond. To ensure close integration with the UK community we have links with the BBSRC Centres in structural biology, which will act as test sites for these developments.