Dr Kevin Cowtan

01904 328253
Email: kevin.cowtan@york.ac.uk

Automated protein structure solution

X-ray crystallography is an important tool in the biochemical and biological sciences for the determination of the 3-dimensional atomic structure of biological molecules. This in turn contributes to the understanding of the function of the molecule, its regulation, and its behaviour within a complex biological system.

The structure solution process involves a number of stages, starting with the laboratory based step of crystallisation and data collection, followed by a number of computational steps involved in the computation of the final atomic model from the X-ray diffraction pattern, via an intermediate stage of a 3-dimensional electron density map. My particular interests are the application of image processing techniques to reduce the noise level in the electron density maps, followed by automated interpretation of protein electron density map in terms of atomic coordinates. I also work with Dr Paul Emsley in the development of new software to visualise, manipulate and validate atomic models.

electron density map Electron density map with protein features overlaid
A portion of an electron density map obtained from an X-ray diffraction experiment at 3.0 Angstrom resolution, and an automatic interpretation of the electron density in terms of protein features, obtained by tracing the connectivity of the protein chain and then correlating electron density features with the known protein sequence.

I have authored several high profile crystallographic software packages, including the "dm" phase improvement software, a suite of crystallographic software libraries ("clipper"), a statistical phase improvement package ("pirate"), and a statistical model building package ("buccaneer"). All of these are distributed through the "CCP4" suite of crystallographic software. I also contribute to the "Coot" molecular graphics software of Dr Paul Emsley. I am also involved with the development of e-Science and Grid-computing tools for crystallography through the e-HTPX project.

I am also involved in training new crystallographers, both through web-based teaching tools, and at a number of international workshops each year. My recent work has been supported by a Royal Society fellowship (2000-2008), BBSRC grant (2008-2013) and a CCP4 fellowship (2013 on).

Selected recent publications

  • Coverage bias in the HadCRUT4 temperature series and its impact on recent temperature trends
    K Cowtan and R G Way (2013) Quarterly Journal of the Royal Meteorological Society in press doi/10.1002/qj.2297/
  • Completion of autobuilt protein models using a database of protein fragments
    K Cowtan (2012) Acta Cryst. D 68, 328-335
  • From crystal to structure with CCP4
    K Cowtan, P Emsley and K S Wilson (2011) Acta Cryst. D 67, 233-234
  • Overview of the CCP4 suite and current developments
    M D. Winn, C C Ballard, K D Cowtan, E J Dodson, P Emsley, P R Evans, R M Keegan, E B Krissinel, A G W Leslie, A McCoy, S J McNicholas, G N Murshudov, N S Pannu, E A Potterton, H R Powell, R J Read, A Vagin and K S Wilson (2011) Acta Cryst. D 67. 235-242
  • Recent developments in classical density modification
    Cowtan K. (2010) Acta Cryst. D 66, 470-478.
  • Features and development of Coot
    P Emsley, B Lohkamp, W G Scott and K Cowtan (2010) Acta Cryst. D 66, 486-501.
  • Ligand Electron Density Shape Recognition Using 3D Zernike Descriptors
    Gunasekaran, S Grandison, K. Cowtan, L. Mak, D. M. Lawson and R. J. Morris (2009)  Lecture Notes in Computer Science 5780, "Pattern Recognition in Bioinformatics", 125-136