Journal Publications, Book Chapters and Selected Reports

Journal articles.
Book chapters.
Selected Reports.
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Journal articles

  1. Flaviu Cipcigan, Anna Paola Carrieri, Ya-Wen Hsiao, Martyn Winn, Edward Pyzer-Knapp, Ritesh Krishna, Max Ryadnov, Colin Edge, Glenn Martyna, and Jason Crain (2018) "Accelerating Molecular Discovery Through Data and Physical Sciences: Applications to Peptide-Membrane Interactions" J. Chem. Phys. 148i, 241744 https://doi.org/10.1063/1.5027261
  2. Ya-Wen Hsiao, Magnus Hedström, Valeria Losasso, Sebastian Metz, Jason Crain and Martyn Winn (2018) "Cooperative Modes of Action of Antimicrobial Peptides Characterized with Atomistic Simulations: a Study on Cecropin B" J. Phys. Chem. B, 122 5908-5921
  3. Will Rowe and Martyn Winn (2018) "Indexed variation graphs for efficient and accurate resistome profiling" Bioinformatics, accepted
  4. Keegan et al. (2018) "Recent developments in MrBUMP: Better search model preparation, graphical interaction with search models, and solution improvement and assessment" Acta Cryst D74, 167-182 https://doi.org/10.1107/S2059798318003455
  5. Potterton et al. (2018) "CCP4i2 - the new graphical user interface to the CCP4 program suite" Acta Cryst D74, 68-84. https://doi.org/10.1107/S2059798317016035
  6. Eugene Krissinel, Ville Uski, Andey Lebedev, Martyn Winn and Charles Ballard (2018) "Distributed Computing for Macromolecular Crystallography" Acta Cryst D74, 143-151. https://doi.org/10.1107/S2059798317014565
  7. Daniel Rigden, Jens Thomas, Felix Simkovic, Adam Simpkin, Martyn Winn, Olga Mayans and Ronan Keegan (2018) "Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE" Acta Cryst D74, 183-193. https://doi.org/10.1107/S2059798318002310
  8. CS Kim, MD Winn, V Sachdeva, KE Jordan (2017) "K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity" BMC Bioinformatics, 18, 467. https://doi.org/10.1186/s12859-017-1881-8
  9. Patwardhan et al. (2017) "Building bridges between cellular and molecular structural biology" eLife, 6, e25835. doi: 10.7554/eLife.25835
  10. Burnley, T., Palmer, C.M. and Winn, M.D. (2017) "Recent developments in the CCP-EM software suite" Acta Cryst. D73 469-477. DOI: 10.1107/S2059798317007859
  11. Joseph, A.P., Lagerstedt, I., Patwardhan, A., Topf, M. and Winn, M.D. (2017) "Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy" J.Struct. Biol. 199, 12-26. DOI: 10.1016/j.jsb.2017.05.007
  12. S Needham, S Roberts, A Arkhipov, V Mysore, C Tynan, L Zanetti-Domingues, E Kim, V Losasso, D Korovesis, M Hirsch, D Rolfe, D Clarke, M Winn, A Lajevardipour, A Clayton, L Pike, M Perani, P Parker, Y Shan, D Shaw, and M Martin-Fernandez (2016) Nature Comms. 7, art. no. 13307. DOI: 10.1038/NCOMMS13307
    - "EGFR oligomerization organizes kinase-active dimers into competent signaling platforms."
  13. Simkovic, F., Thomas, J. M. H., Keegan, R. M., Winn, M. D., Mayans, O. and Rigden, D. J. IUCrJ, 3, 259 - 270 (2016)
    - "Residue contacts predicted by evolutionary covariance extend the application of ab initio Molecular Replacement to larger and more challenging protein folds"
  14. Agnel P Joseph, Sony Malhotra, Tom Burnley, Chris Wood, Daniel K Clare, Martyn Winn, and Maya Topf, Methods, 100, 42-49 (2016)
    - "Refinement of atomic models in high resolution EM reconstructions using Flex-EM and local assessment" doi: 10.1016/j.ymeth.2016.03.007
  15. A. Cheng, R. Henderson, D. Mastronarde, S.J. Ludtke, R.H. Schoenmakers, J. Short, R. Marabini, S. Dallakyan, D. Agard and M.D. Winn. J. Struct. Biol., 192, 146-150 (2015)
    - "MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography" doi:10.1016/j.jsb.2015.04.002
  16. Thomas, J. M. H., Keegan, R. M., Bibby, J., Winn, M. D., Mayans, O. and Rigden, D. J. IUCrJ, 2, 198-206 (2015)
    - "Routine phasing of coiled-coil protein crystal structures with AMPLE" doi:10.1107/S2052252515002080
  17. O.C.Coban et al., Biophys.J., 108, 1013-1026 (2015)
    - "Effect of phosphorylation on the EGFR dimer stability probed by single-molecule dynamics and FRET/FLIM" doi:10.1016/j.bpj.2015.01.005
  18. R.M.Keegan, J. Bibby, J. Thomas, D. Xu, Y. Zhang, O. Mayans, M.D.Winn and D.J.Ridgen, Acta Cryst., D71, 338-43 (2015)
    - "Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models" [ DOI: 10.1107/S1399004714025784 ]
  19. C. Wood, T. Burnley, A. Patwardhan, S. Scheres, M. Topf, A. Roseman and M.D.Winn, Acta Cryst., D71, 123 - 126 (2015)
    - "Collaborative Computational Project for Electron cryo-Microscopy" [ DOI: 10.1107/S1399004714018070 ]
  20. V. Sachdeva, C.S. Kim, K. E. Jordan and M.D.Winn, Proceedings of the Thirteenth IEEE International Workshop on High Performance Computational Biology
    - "Parallelization of the Trinity pipeline for de novo transcriptome assembly"
    10.1109/IPDPSW.2014.67
  21. Tai Kiuchi et al., Sci. Signal., 7, ra78 (2014)
    - "The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility." [ DOI: 10.1126/scisignal.2005157 ]
  22. Kinya Hotta, Ronan M. Keegan, Soumya Ranganathan, Minyi Fang, Jaclyn Bibby, Martyn D. Winn, Michio Sato, Mingzhu Lian, Kenji Watanabe, Daniel J. Rigden, and Chu- Young Kim, Angew. Chem. Int. Ed., 53, 824-828 (2014)
    - "Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis" [ doi:10.1002/anie.201307404 ]
  23. J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden, Acta. Cryst. D69, 2194-2201 (2013)
    - "Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement"
  24. H.H.Loeffler and M.D.Winn, PROTEINS: Structure, Function, and Bioinformatics, 81, 1931-1943 (2013)
    - "Ligand Binding and Dynamics of the Monomeric Epidermal Growth Factor Receptor Ectodomain" [ doi: 10.1002/prot.24339 ]
  25. Ardan Patwardhan, Jose-Maria Carazo, Bridget Carragher, Richard Henderson, J Bernard Heymann, Emma Hill, Grant J Jensen, Ingvar Lagerstedt, Catherine L Lawson, Steven J Ludtke, David Mastronarde, William J Moore, Alan Roseman, Peter Rosenthal, Carlos-Oscar S Sorzano, Eduardo Sanz-Garcia, Sjors H W Scheres, Sriram Subramaniam, John Westbrook, Martyn Winn, Jason R Swedlow and Gerard J Kleywegt, Nature Structural & Molecular Biology, 19, 1203-1207 (2012)
    Data management challenges in three-dimensional EM
  26. J. Bibby, R. M. Keegan, O. Mayans, M. D. Winn and D. J. Rigden, Acta. Cryst. D68 , 1622-1631 (2012)
    - "AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models" [ doi:10.1107/S0907444912039194 ]
       reprint in PDF format Copyright © International Union of Crystallography
  27. SK Roberts, CJ Tynan, M Winn, and ML Martin-Fernandez, Biochem. Soc. Trans. 40, 189-194 (2012)
    - "Investigating extracellular in situ EGFR structure and conformational changes using FRET microscopy" [doi: 10.1042/BST20110632]
  28. Christopher J. Tynan, Selene K. Roberts, Daniel J. Rolfe, David T. Clarke, Hannes H. Loeffler, Johannes Kaestner, Martyn D. Winn, Peter J. Parker, and Marisa L. Martin-Fernandez Mol.Cell.Biol. 31, 2241-2252 (2011)
    - "Human-EGFR aligned on the plasma membrane adopts key features of Drosophila-EGFR asymmetry" [ doi:10.1128/MCB.01431-10 ]
  29. M. D. Winn et al. Acta. Cryst. D67 , 235-242 (2011)
    - "Overview of the CCP4 suite and current developments" [ doi:10.1107/S0907444910045749 ]
       reprint in PDF format Copyright © International Union of Crystallography
  30. Garib N. Murshudov, Pavol Skubak, Andrey A. Lebedev, Navraj S. Pannu, Roberto A. Steiner, Robert A. Nicholls, Martyn D. Winn, Fei Long and Alexei A. Vagin Acta. Cryst. D67 , 355-367 (2011)
    - "REFMAC5 for the refinement of macromolecular crystal structures" [ doi:10.1107/S0907444911001314 ]
       reprint in PDF format Copyright © International Union of Crystallography
  31. R. M. Keegan, F. Long, V. J. Fazio, M. D. Winn, G. N. Murshudov and A. A. Vagin Acta. Cryst. D67 , 313-323 (2011)
    - "Evaluating the solution from MrBUMP and BALBES" [ doi:10.1107/S0907444911007530 ]
  32. J. J. Lovelace, M. D. Winn and G. E. O. Borgstahl J.App.Cryst. 43 285-292, (2010)
    - "Simulation of modulated reflections" [ doi:10.1107/S0021889810001846 ]
       reprint in PDF format Copyright © International Union of Crystallography
  33. Johannes Kaestner, Hannes H Loeffler, Selene K Roberts, Marisa L Martin-Fernandez and Martyn D Winn J. Struct. Biol., 167 117-128 (2009)
    - "Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics"
    http://dx.doi.org/10.1016/j.jsb.2009.04.007
  34. M.Vollmar, D. Schlieper, M. Winn, C. Buechner and G.Groth, J. Biol. Chem., 284, 18228-18235 (2009)
    - "Structure of the C14-rotor ring of the proton translocating chloroplast ATP synthase"
  35. E. Vandermarliere, T.M. Bourgois, M.D. Winn, S. Van Campenhout, G. Volckaert, J.A. Delcour, S.V. Strelkov, A.Rabijns and C.M. Courtin Biochemical Journal 418, 39-47 (2009)
    - "Structure of Bacillus subtilis GH family 43 arabinoxylan arabinofuranohydrolase"
  36. D.J Rigden, R.M Keegan and M.D Winn Acta Cryst. D64 1288-1291 (2008)
    - "Molecular Replacement using ab initio polyalanine models generated with ROSETTA"
       reprint in PDF format Copyright © International Union of Crystallography
  37. Stephen E.D. Webb, Selene K. Roberts, Sarah R. Needham, Christopher J. Tynan, Daniel J. Rolfe, Martyn D. Winn, David T. Clarke, Roger Barraclough, and Marisa L. Martin-Fernandez Biophys. J. 94, 803-819 (2008)
    - "Single molecule imaging and FLIM show different structures for high and low-affinity EGFRs in A431 cells"
  38. Keegan, R.M. and Winn, M.D. Acta Cryst. D64, 119-124 (2008)
    - "MrBUMP: An automated pipeline for molecular replacement"
       reprint in PDF format Copyright © International Union of Crystallography
  39. McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C. and Read, R.J. J.App.Cryst. 40, 658-674 (2007)
    - "Phaser crystallographic software"
  40. R.M.Keegan and M.D.Winn, Acta Cryst. D63, 447 - 457 (2007)
    - "Automated search-model discovery and preparation for structure solution by molecular replacement"
       reprint in PDF format Copyright © International Union of Crystallography
  41. Bahar, M., Ballard, C.C., Cohen, S., Cowtan, K., Dodson, E.J., Emsley, P., Esnouf, R.M., Keegan, R.M., Lamzin, V., Langer, G., Levdikov, V., Long, F., Meier, C.J., Muller, A., Murshudov, G., Perrakis, A., Siebold, C., Stein, N.D., Turkenburg, M.G.W., Vagin, A., Winn, M.D., Winter, G. and Wilson, K.S. (2006) Acta Cryst. D62, 1170-1183
    - "SPINE workshop on automated X-ray analysis: a progress report"
  42. 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, Acta Cryst. D60, 2250 - 2255 (2004)
    - "The new CCP4 Coordinate Library as a toolkit for the design of coordinate-related applications in protein crystallography."
  43. M.D.Winn, J. Synchrotron Rad. 10, 23-25 (2003)
    - "An overview of the CCP4 project in Protein Crystallography: an example of a collaborative project"
       reprint in PDF format Copyright © International Union of Crystallography
  44. M.D.Winn, A. W. Ashton, P. J. Briggs, C. C. Ballard and P. Patel, Acta Cryst. D58 1929-1936 (2002)
    - "On-going developments in CCP4 for high-throughput structure determination"
       
    reprint in PDF format Copyright © International Union of Crystallography
  45. D.R.Hall, J.Haddon, G.A.Leonard, S.Bailey, M.Neu, M.D.Winn and P.F.Lindley, Acta Cryst. D58, 70 - 80 (2002)
    - "The Crystal and Molecular Structures of Diferric Porcine and Rabbit Serum Transferrins at resolutions of 2.15 A and 2.60 A respectively"
  46. M.D.Winn, M.N.Isupov and G.N.Murshudov, Acta Cryst. D57, 122 - 133 (2001).
    - "Use of TLS parameters to model anisotropic displacements in macromolecular refinement"
       reprint in PDF format Copyright © International Union of Crystallography
  47. J.-L. Lopez-Martin, E. Lomba, G. Kahl, M.D. Winn, and M. Rassinger, J.Phys.:Condens.Matter 9, 3321 (1997).
    - "An integral-equation approach to the electronic structure of liquid silicon"
  48. M.D.Winn, M.Rassinger and J.Hafner, Phys.Rev.B 55, 5364 (1997).
    - "The atomic and electronic structure of the diamond (100) surface: reconstructions and rearrangements at high hydrogen coverage."
  49. M.D.Winn and M.Rassinger, Europhys.Lett. 32, 55 (1995).
    - "Structure and Dynamics of Diamond (100) Surfaces at High Hydrogen Coverage"
  50. M.D.Winn and G.Kahl, J.Chem.Phys. 101 10850, (1994).
    - "A nonlinear integral equation theory for the optical dielectric properties of a polarisable fluid"
  51. M.D.Winn and G.Kahl, J.Chem.Phys. 100, 7836 (1994).
    - "A self-consistent determination of the atomic and electronic structure of a model liquid metal"
  52. M.D.Winn and G.Kahl, J.Chem.Phys. 100, 7567 (1994).
    - "Application of classical liquid state methods to the calculation of optical absorption bands in fluids"
  53. M.D.Winn and D.E.Logan, J.Phys.:Condens.Matter 5, 3121 (1993).
    - "The dipolar Frenkel excitonic insulator phase of an impurity in a liquid solvent: results"
  54. M.D.Winn and D.E.Logan, J.Phys.:Condens.Matter 5, 3103 (1993).
    - "The dipolar Frenkel excitonic insulator phase of an impurity in a liquid solvent: theory"
  55. M.D.Winn and D.E.Logan, J.Phys.:Condens.Matter 4, 5509 (1992).
    - "On the formation and nature of a dipolar Frenkel excitonic insulator"
  56. M.D.Winn and D.E.Logan, J.Chem.Phys. 96, 4818 (1992).
    - "Comment on: Recent calculations of liquid-state band structures"
  57. M.D.Winn and D.E.Logan, J.Chem.Phys. 93, 6756 (1990).
    - "Localization versus band-crossing transitions in a multiband model of spatially disordered materials"
  58. M.D.Winn and D.E.Logan, Phys.Chem.Liq. 22, 11 (1990).
    - "Localization in spatially disordered system: screening and band structure effects at the EMA level"
  59. I.J.Bush, D.E.Logan, P.A.Madden and M.D.Winn, J.Phys.:Condens.Matter 1, 8735 (1989).
    - "The EMA for a two-band spatially disordered system: comparison of simulation with theory"
  60. M.D.Winn and D.E.Logan, J.Phys.:Condens.Matter 1, 8683 (1989).
    - "Soluble theories for the density of states of a spatially disordered two-level tight-binding model"
  61. I.J.Bush, D.E.Logan, P.A.Madden and M.D.Winn, J.Phys.:Condens.Matter 1, 2551 (1989).
    - "The density of states of a spatially disordered system: theory compared with simulation"
  62. M.D.Winn and D.E.Logan, J.Phys.:Condens.Matter 1, 1753 (1989).
    - "A soluble theory for the density of states of a spatially disordered system"
  63. D.E.Logan and M.D.Winn, J.Phys.C:Solid State 21, 5773 (1988).
    - "The density of states of a spatially disordered tight-binding model"

Book chapters

  1. Marisa L. Martin-Fernandez, David T. Clarke, Michael Hirsch, Sarah R. Needham, Selene K. Roberts, Daniel J. Rolfe, Chris J. Tynan, Stephen E.D. Webb, Martyn Winn, and Laura Zanetti Domingues (2012) in Molecular Imaging, ISBN 978-953-51-0359-2, edited by Bernhard Schaller.
    - "Investigating the Conformation of HER Membrane Proteins in Cells via Single Molecule and FLIM Microscopy"
  2. D.T. Clarke, D. Rolfe, S.E.D. Webb, M. Winn and M. L. Martin-Fernandez (2010) in "MICROSCOPY: SCIENCE, TECHNOLOGY, APPLICATIONS AND EDUCATION" eds A. Mendez-Vilas and J.Diaz, published by Formatex Research Center
    - "Single molecule fluorescence imaging of receptor interactions in mammalian cell signalling"
  3. M.D.Winn, G.N.Murshudov and M.Z.Papiz, Methods in Enzymology 374 300-321 (2003)
    - "Macromolecular TLS refinement in REFMAC at moderate resolutions"
  4. E.J.Dodson, M.D.Winn and A.C.Ralph, Methods in Enzymology 277, 620-633 (1997).
    - "A Collaborative Computational Project, Number 4: Providing Programs for Protein Crystallography"

Selected Reports

  1. Hannes H. Loeffler and Martyn D. Winn, DL Technical Reports, DL-TR-2009-002 (2009)
    Large Biomolecular Simulation on HPC Platforms I. Experiences with AMBER, Gromacs and NAMD
  2. H.H. Loeffler, J. Kästner, M.D. Winn, M.L. Martin-Fernandez and S.K. Roberts, Fontiers 2008, 18-19
    - "Larger and longer: atomistic and coarse-grained simulations of the Epidermal Growth Factor Receptor"
  3. R.M. Keegan and M. D. Winn, Fontiers 2008, 20-21
    - "CCP4 6.1: improved algorithms and new tools for experimental protein structure determination"
  4. "Understanding cancer with supercomputers", Science and Technology Facilities Council Annual Report and Accounts 2007-2008, p24.
  5. M D Winn, Fontiers 2006, 16-17
    - "CCP4 6.0: State-of-the-art Software for the Experimental Determination of Protein Structures"
  6. Rob Allan, Colin Nave, Ronan Keegan, Dave Meredith, Martyn Winn, Graeme Winter, Oleg Dolomanov, Ludovic Launer, Paul Young, Ian Berry (2005), Proceedings of the UK e-science All Hands Meeting
    http://www.allhands.org.uk/2005/proceedings/papers/385.pdf
    Portal Design, Synchrotron and HPC Services in e-HTPX - A resource for High Throughput Protein Crystallography
  7. Rob Allan, Ronan Keegan, Dave Meredith, Martyn Winn, Graeme Winter, Jon Diprose, Chris Mayo, Ludovic Launer, Joel Fillon, Paul Young (2004), Proceedings of the UK e-science All Hands Meeting
    http://www.allhands.org.uk/2004/proceedings/papers/101.pdf
    e-HTPX - HPC, Grid and Web-Portal Technologies in High Throughput Protein Crystallography
  8. M.D.Winn, SRD Annual Report 2003-2004, e-HTPX: Automation and e-Science for Protein Crystallography
  9. M.D.Winn and I.J.Bush, SRD Annual Report 2002-2003, Biology from First Principles: Quantum Mechanical Studies of the Crystal Structure of Crambin
  10. M.D.Winn, CCP4 Newsletter 39, March 2001, ANISOANL - analysing anisotroptic displacement parameters

martyn.winn at stfc.ac.uk
Last modified: Sat Jan 24 22:32:32 GMT 2015