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Publications relating to CCPN software development in peer reviewed journals

Publications from CCPN

A complete list of all published articles relating to CCPN where the developers are in the author list.
  • AnalysisAssign: A Flexible Platform for Integrated NMR Analysis
    Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, Vuister GW.

    J. Biomol. NMR
    2016
    , 66:2 111–124.
  • NMR Exchange Format: a unified and open standard for representation of NMR restraint data.
    Gutmanas A, Adams PA, Bardiaux B, Berman HA, Case DA, Fogh RH, Guntert P, Hendrickx PMS, Herrmann T, Kleywegt G, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CS, Tejero R, Ulrich E, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, and Vuister GW
    Nature Struct Biol 2015 June 22:6 :433-4. DOI:10.1038/nsmb.3041
  • The Second Round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013
    Rosato A, Vranken W, Fogh RH, Ragan TJ, Tejero R, Pederson K, Lee H-W, Prestegard JH, Yee A, Wu B, Lemak A, Houliston S, Arrowsmith CH, Kennedy M, Acton TB, Xiao R, Liu G, Montelione GT, and Vuister GW
    J Biomol NMR 2015 June
  • Analysis of the structural quality of the CASD-NMR 2013 entries
    Ragan TJ, Fogh, RH, Tejero R, Vranken W, Montelione GT, Rosato A, Vuister GW
    J Biomol NMR 2015 June DOI:10.1007/s10858-015-9949-0
  • Structure calculation, refinement and validation using CcpNmr Analysis
    Skinner SP, Goult BT, Fogh RH, Boucher W, Stevens TJ, Laue ED, and Vuister GW
    Acta Cryst 2015 D71 154-161 view the article
  • Python Programming for Biology - Bioinformatics and beyond.
    Stevens TJ and Boucher W
    Cambridge University Press, Cambridge, UK;  February 2015. ISBN 9780521720090.
  • An overview of tools for the validation of protein NMR structures
    Vuister GV, Fogh RH, Hendrickx PMS, Doreleijers JF, and Gutmanas A
    J Biomol NMR 2014 April 58:4 259-285 view the article
  • High-Resolution Heteronuclear Multidimensional NMR of Proteins in Living Insect Cells Using a Baculovirus Protein Expression System. 
    Jumpei Hamatsu, Daniel O’Donovan, et al.
    J. Am. Chem. Soc., 2013 135 (5), pp 1688–1691 view the article
  • Wenmr: Structural biology on the grid 
    Wassenaar TA, Van Dijk M, Vranken VF, Vuister GW, Fogh RH, Ionides J, Laue ED, Spronk C, Bonvin AMJJ et al.
    J Grid Computing, 2012 Nov DOI 10.1007/s10723-012-9246-z view the article
  • Structure Simulation with Calculated NMR Parameters — Integrating COSMOS into the CCPN Framework
    I
    Studies in Health Technology and Informatics, 2012 May 175: 162-172. view the article
  • EUROCarbDB: An open-access platform for glycoinformatics.
    von der Lieth C-W, Fogh RF, Ionides J, Lundborg M, Vranken VF, Haslam SM et al.
    Glycobiology, 2011 April. 21(4): 493-502. view the article
  • A software framework for analysing solid-state MAS NMR data.
    Stevens TJ, Fogh RH, Boucher W, Higman VA, Eisenmenger F, Bardiaux B, van Rossum BJ, Oschkinat H, Laue ED. 
    J Biomol NMR
    .
    2011 Sep 28. 51(4): 437-447. view the article

  • The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR.
    Chignola F, Mari S, Stevens TJ, Fogh RH, Mannella V, Boucher W, Musco G.
    Bioinformatics. 2011 Jan 6; 27(6): 885-886. view the article.
  • Straightforward and complete deposition of NMR data to the PDBe.
    Penkett CJ, van Ginkel G, Velankar S, Swaminathan J, Ulrich EL, Mading S, Stevens TJ, Fogh RH, Gutmanas A, Kleywegt GJ, Henrick K, Vranken WF.
    J Biomol NMR. 2010 Oct;48(2):85-92. view the article
  • MEMOPS: data modelling and automatic code generation.
    Fogh RH, Boucher W, Ionides JM, Vranken WF, Stevens TJ, Laue ED.
    J Integr Bioinform. 2010 Mar 25;7(3). view the article
  • A nomenclature and data model to describe NMR experiments.
    Fogh RH, Vranken WF, Boucher W, Stevens TJ, Laue ED.
    J Biomol NMR. 2006 Nov;36(3):147-55. view the article
  • The CCPN data model for NMR spectroscopy: development of a software pipeline.
    Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED.
    Proteins. 2005 Jun 1;59(4):687-96. view the article
  • A framework for scientific data modeling and automated software development.
    Fogh RH, Boucher W, Vranken WF, Pajon A, Stevens TJ, Bhat TN, Westbrook J, Ionides JM, Laue ED.
    Bioinformatics. 2005 Apr 15;21(8):1678-84 view the article
  • Design of a data model for developing laboratory information management and analysis systems for protein production.
    Pajon A, Ionides J, Diprose J, Fillon J, Fogh R, Ashton AW, Berman H, Boucher W, Cygler M, Deleury E, Esnouf R, Janin J, Kim R, Krimm I, Lawson CL, Oeuillet E, Poupon A, Raymond S, Stevens T, van Tilbeurgh H, Westbrook J, Wood P, Ulrich E, Vranken W, Xueli L, Laue E, Stuart DI, Henrick K.
    Proteins
    .
    2005 Feb 1;58(2):278-84. view the article
  • Memops: Data modeling and automatic code generation in multiple languages.
    Fogh RH, Boucher W, Vranken WF, Pajon A, Stevens TJ, Bhat TN, Westbrook J, Ionides JM, Laue ED.
    Proceedings of Second European Workshop on Model Driven Architecture (MDA) (D.H. Akehurst, ed.)
    Technical Report 17-04, University of Kent, Computing Laboratory. 2004 pp 116-123 view the article
  • The CCPN project: an interim report on a data model for the NMR community.
    Fogh R, Ionides J, Ulrich E, Boucher W, Vranken W, Linge JP, Habeck M, Rieping W, Bhat TN, Westbrook J, Henrick K, Gilliland G, Berman H, Thornton J, Nilges M, Markley J, Laue E.  
    Nat Struct Biol. 2002 Jun;9(6):416-8. view the article
  • BBSRC Business, July 2001
    Collaboration to make the most of NMR
J Biomol NMR 2014