Computational Biology Group

Summary

Model
of a fluorophore
A molecular model of a fluorophore
(Credit: Martyn Winn, STFC)

The Computational Biology Group, a part of the Applications Division, develops and applies computational methods for understanding the molecular basis of life. We develop software for processing various kinds of experimental data, and for organising storage of data. We also have expertise in modelling and simulating biological systems.

Our work contributes to the fundamental understanding of how genes and proteins operate, and has applications in drug development, crop science and environmental monitoring. We are particularly interested in computationally challenging problems, and apply high performance computing and data intensive computing methods.

Projects

The group consists of a number of project teams, based on both the Daresbury and Rutherford Appleton Laboratory sites. Current projects include:

  • Sequencing and bioinformatics: High throughput sequencing technologies are making a big impact in many areas of life sciences. We are focussing initially on transcriptomics in which the mRNA corresponding to transcribed genes is sequenced. Working with collaborators from IBM and Rothamsted Research, as part of a Hartree Centre project, we have worked on improving the computational efficiency of the popular Trinity pipeline.
     
  • Macromolecular Crystallography: We host the core group for CCP4 which develops and maintains a software suite for solving protein structures via X-ray crystallography. CCP4 is the longest running Collaborative Computational Project, and supports a lively worldwide community of crystallographers.
     
  • Electron cryo-microscopy: We are setting up the CCP-EM project providing computational support for biological electron cryo-microscopy. This rapidly growing technique provides detailed structural information on protein complexes, viruses and molecular machines.
     
  • Protein Data Management: PiMS is a laboratory information management system for protein scientists. The PiMS software enables researchers to enter data, track samples and report results during the production of recombinant proteins for structural and functional applications.
     
  • Biomolecular simulation: We provide general support to the biomolecular simulation community through two EPSRC-funded projects: CCP-BioSim is the Collaborative Computational Project for Biomolecular Simulation, and HEC-BioSim is the High-End Computing consortium for biomolecular simulation. We also have an on-going research programme into the Epidermal Growth Factor Receptor, in collaboration with the microscopy group of Marisa Martin-Fernandez in CLF.
     
  • Computational Structural Biology: Instruct is the European infrastructure project for structural biology. We host the computational centre of Instruct, providing expertise in computational structural biology. We also represent Instruct in the BioMedBridges project, which is looking at building data bridges between different biomedical science domains.

Image and caption

A molecular model of a fluorophore - inhibitor conjugate (stick representation) bound to the kinase domain of Epidermal Growth Factor Receptor (surface representation). The EGFR family of protein receptors are implicated in a number of cancers, and the inhibitor is the licensed cancer drug Iressa. The fluorophore is used by collaborators in the Central Laser Facility of STFC to monitor the receptors in live cells. The image was generated by molecular graphics software from the CCP4 project.
Credit: Martyn Winn, STFC

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