Publications

Papers:

The reference for the `dm' software is (2). The reference for the `fffear' software is (11). The reference for the `pirate' software is (14). The reference for the `buccaneer' software is (24).

  1. Cowtan K., Main P. (1993) Acta Cryst. D49, 148-157. Improvement of macromolecular electron density maps by the simultaneous application of real and reciprocal space constraints. (abstract)
  2. Cowtan K. (1994), Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-38. 'dm': An automated procedure for phase improvement by density modification. (ps)
  3. Cowtan K., Main P. (1996) Acta Cryst. D52, 43-48. Phase Combination and Cross Validation in Iterated Density Modification Calculations. (abstract)
  4. Cowtan K., Main P. (1998) Acta Cryst. D54, 487-493. Miscellaneous algorithms for density modification. (abstract)
  5. Cowtan K. (1998) Acta Cryst. D54, 750-756. Modified phased translation functions and their application to molecular fragment location. (abstract)
  6. Cowtan K. (1999) Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 36, 31-35. Recent improvements to the `dm' package. (html)
  7. Cowtan K. (1999) Acta Cryst. D55, 1555-1567. Error Estimation and Bias Correction in Phase Improvement Calculations. (abstract)
  8. Cowtan K. (2000) Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 38. Gaussian Likelihoods in real and reciprocal space. (html)
  9. Cowtan K., Ten Eyck L. F. (2000) Acta Cryst. D56, 842-856. Eigensystem Analysis of the Refinement of a Small Metalloprotein. (html/pdf)
  10. Cowtan K. (2000) Acta Cryst. D56, 1612-1621. General quadratic functions in real and reciprocal space and their application to likelihood phasing. (html/pdf)
  11. Cowtan K. (2001) Acta Cryst. D57, 1435-1444. Fast Fourier feature recognition (html/pdf)
  12. Cowtan K. (2002) Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 40. The Clipper Project (html)
  13. Cowtan K. (2002) Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 40. FFFEAR (html)
  14. Cowtan K. (2002) J. Appl. Cryst. 35, 655-663. Generic representation and evaluation of properties as a function of position in reciprocal space.
  15. Cowtan K. (2002) Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 41. Handling reflection data using the Clipper libraries. (html)
  16. E. Potterton, S. McNicholas, E. Krissinel, K. Cowtan and M. Noble (2002) Acta Cryst. D58, 1955-1957. The CCP4 molecular-graphics project. (html/pdf)
  17. Cowtan K. (2003) IUCr Computing Commission Newsletter, 2, The Clipper C++ libraries for X-ray crystallography, 4-9 (pdf)
  18. L. Potterton, S. McNicholas, E. Krissinel, J. Gruber, K. Cowtan, P. Emsley, G. N. Murshudov, S. Cohen, A. Perrakis and M. Noble (2004) Acta Cryst. D60, 2288-2294. Developments in the CCP4 molecular-graphics project (pdf)
  19. E. B. Krissinel, M. D. Winn, C. C. Ballard, A. W. Ashton, P. Patel, E. A. Potterton, S. J. McNicholas, K. D. Cowtan and P. Emsley (2004) Acta Cryst. D60, 2250-2255. The new CCP4 Coordinate Library as a toolkit for the design of coordinate-related applications in protein crystallography (pdf)
  20. P. Emsley and K. Cowtan (2004) Acta Cryst. D60, 2126-2132. Coot: model-building tools for molecular graphics (pdf)
  21. B. Lohkamp, P. Emsley, and K. Cowtan (2005) CCP4 Newsletter, 42, Summer 2005, Coot News. (pdf)
  22. K.Cowtan (2005) J. Appl. Cryst. 38, 193-198. Likelihood weighting of partial structure factors using spline coefficients (pdf)
  23. K. Cowtan (2006) CCP4 Newsletter, 44, Summer 2006, The "Buccaneer" protein model building software. (pdf)
  24. K. Cowtan (2006) Acta Cryst. D62, 1002-1011. The Buccaneer software for automated model building (pdf)
  25. M. Bahar, C. Ballard, S. X. Cohen, K. D. Cowtan, E. J. Dodson, P. Emsley, R. M. Esnouf, R. Keegan, V. Lamzin, G. Langer, V. Levdikov, F. Long, C. Meier, A. Muller, G. N. Murshudov, A. Perrakis, C. Siebold, N. Stein, M. G. W. Turkenburg, A. A. Vagin, M. Winn, G. Winter and K. S. Wilson (2006) Acta Cryst. D62, 1170-1183. SPINE workshop on automated X-ray analysis: a progress report (pdf)
  26. D. Watts, K. Cowtan and J. Wilson (2008) J. Appl. Cryst. 41, 8-17.Automated classification of crystallization experiments using wavelets and statistical texture characterization techniques (pdf)
  27. K. Cowtan (2008) Acta Cryst. D64, 83-89. Fitting molecular fragments into electron density (pdf)
  28. P. 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. Ligand Electron Density Shape Recognition Using 3D Zernike Descriptors
  29. Cowtan K. (2010) Acta Cryst. D66, 470-478. Recent developments in classical density modification (pdf)
  30. P. Emsley, B. Lohkamp, W. G. Scott and K. Cowtan (2010) Acta Cryst. (2010). D66, 486-501. Features and development of Coot (pdf)

Reviews:

  1. Zhang K. Y. J., Cowtan K., Main P. (1997) Methods in Enzymology, 277, 53-64. Combining constraints for electron-density modification.
  2. Cowtan K., Zhang K. Y. J. (1999) Progress in Biophysics and Molecular Biology, 72, 245-270. Density Modification for macromolecular phase improvement.
  3. Zhang K. Y. J., Cowtan K. D., Main P. (2001) "International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules." Rossmann, M. G. and Arnold, E., Editors. Dordrecht: Kluwer Academic Publishers, The Netherlands. Chapter 15.1. Density Modification.
  4. Cowtan K. D., Zhang K. Y. J., Main P. (2001) "International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules." Rossmann, M. G. and Arnold, E., Editors. Dordrecht: Kluwer Academic Publishers, The Netherlands. Chapter 25.2.5. DM/DMMULTI software for phase improvement by density modification.
  5. Cowtan K. D. (2001) "Encyclopedia of Life Sciences" New York: MacMillan. The phase problem and its solution.
  6. Cowtan, K. (2003) Crystallography Reviews, 9, 73-80. An Overview of Some Developments in Crystallographic Computing Methods Worldwide.

Conference proceedings:

  1. Cowtan K. D. (1992) Crystallographic Computing 5: From Chemistry to Biology Edited. by D. Moras, A. D. Podjarny, and J. C. Thierry. Sayre's equation and histogram methods for phase refinement and extension of protein structures.
  2. Cowtan K. D. (1997) Macromolecular Refinement: Proceedings of the CCP4 Study Weekend, January 1996 (CCLRC) 23-28. Cross-Validation and the Free-R. (ps)
  3. Cowtan K. D. (1998) Direct Methods for Solving Macromolecular Structures: A NATO ASI Series (Springer-Verlag). Introduction to Density Modification.
  4. Cowtan K. D. (1998) Direct Methods for Solving Macromolecular Structures: A NATO ASI Series (Springer-Verlag). Density Modification and Direct Methods.
  5. Naismith J., Cowtan K., Ashton A. (2001) Acta Cryst. D57, part 10. Molecular replacement and its relatives. J. Naismith, K. Cowtan and A. Ashton
  6. Cowtan K. (2004) Acta Cryst. A60, s14. Statistical phase improvement without a solvent boundary.
  7. Cowtan K. (2006) Abstracts of the 8th International School on the Crystallography of Biological macromolecules, Como, Italy, 21-25th May 2006: Optimal statistical targets for phase improvement and model building.

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