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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.

 

CcpNmr AnalysisScreen, a new software programme with dedicated automated analysis tools for fragment-based drug discovery by NMR.
Mureddu LG, Ragan TJ, Brooksbank EJ, and Vuister GW.
2020 Journal of Biomolecular NMR, 74, 565-577. view article

Simple high-resolution NMR spectroscopy as a tool in molecular biology.
Mureddu L, and Vuister GW.
2019 FEBS Journal, 286(11), 2035–2042. view article

CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis.
Skinner SP, Fogh RH, Boucher W, Ragan TJ, Mureddu LG, and Vuister GW.
2016 Journal of Biomolecular NMR, 66(2), 111–124. view article

NMR Exchange Format: A unified and open standard for representation of NMR restraint data.
Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PMS, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW.
2015 Nature Structural and Molecular Biology, 22(6), 433–434. view article

Analysis of the structural quality of the CASD-NMR 2013 entries.
Ragan TJ, Fogh RH, Tejero R, Vranken W, Montelione GT, Rosato A, and Vuister GW.
2015 Journal of Biomolecular NMR, 62(4), 527–540. view article

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 HW, 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.
2015 Journal of Biomolecular NMR, 62(4), 413–424. view article

Structure calculation, refinement and validation using CcpNmr Analysis.
Skinner SP, Goult BT, Fogh RH, Boucher W, Stevens TJ, Laue ED, and Vuister GW.
2015 Acta Crystallographica Section D: Biological Crystallography, 71, 154–161. view article

Python Programming for Biology – Bioinformatics and byond.
Stevens TJ, and Boucher W.
2015 Cambridge University Press, Cambridge, UK. view book at publisher

An overview of tools for the validation of protein NMR structures.
Vuister GW, Fogh RH, Hendrickx PMS, Doreleijers JF, and Gutmanas A.
2014 Journal of Biomolecular NMR, 58(4), 259–285. view article

High-resolution heteronuclear multidimensional NMR of proteins in living insect cells using a baculovirus protein expression system.
Hamatsu J, O’Donovan D, Tanaka T, Shirai T, Hourai Y, Mikawa T, Ikeya T, Mishima M, Boucher W, Smith BO, Laue ED, Shirakawa M, and Ito Y.
2013 Journal of the American Chemical Society, 135(5), 1688–1691. view article

Structure Simulation with Calculated NMR Parameters - Integrating COSMOS into the CCPN Framework.
Schneider O, Fogh RH, Sternberg U, Klenin K, and Kondov I.
2012 Studies in Health Technology and Informatics, 175, 162–172. view article

WeNMR: Structural Biology on the Grid.
Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A, Ferella L, Rosato A, Bertini I, Herrmann T, Jonker HRA, Bagaria A, Jaravine V, Güntert P, Schwalbe H, Vranken WF, Doreleijers JF, Vriend G, Vuister GW, Franke D, Kikhney A, Svergun DI, Fogh RH, Ionides J, Laue ED, Spronk C, Jurkša S, Verlato M, Badoer S, Dal Pra S, Mazzucato M, Frizziero E, Bonvin AMJJ.
2012 Journal of Grid Computing, 10(4), 743–767. view 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, and Musco G.
2011 Bioinformatics, 27(6), 885–886. view 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 B-J, Oschkinat H, and Laue ED.
2011 Journal of Biomolecular NMR, 51(4), 437–447. view article

EUROCarbDB: An open-access platform for glycoinformatics.
Von Der Lieth CW, Freire AA, Blank D, Campbell MP, Ceroni A, Damerell DR, Dell A, Dwek RA, Ernst B, Fogh R, Frank M, Geyer H, Geyer R, Harrison MJ, Henrick K, Herget S, Hull WE, Ionides J, Joshi HJ, Kamerling JP, Leeflang BR, Lütteke T, Lundborg M, Maass K, Merry A, Ranzinger R, Rosen J, Royle L, Rudd PM, Schloissnig S, Stenutz R, Vranken WF, Widmalm G, Haslam SM.
2011 Glycobiology, 21(4), 493–502. view article

MEMOPS: data modelling and automatic code generation.
Fogh RH, Boucher W, Ionides JMC, Vranken WF, Stevens TJ, and Laue ED.
2010 Journal of Integrative Bioinformatics, 7(3). view 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, and Vranken WF.
2010 Journal of Biomolecular NMR, 48(2), 85–92. view article

Nomenclature and data model to describe NMR experiments.
Fogh RH, Vranken WF, Boucher W, Stevens TJ, and Laue ED.
2006 A Journal of Biomolecular NMR, 36(3), 147–155. view 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 JMC, and Laue ED.
2005 Bioinformatics, 21(8), 1678–1684. view 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.
2005 Proteins: Structure, Function and Genetics, 58(2), 278–284. view 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, and Laue ED.
2005 Proteins: Structure, Function and Genetics, 59(4), 687–696. view article

Memops: Data modeling and automatic code generation in mulitple languages.
Fogh RH, Boucher W, Vranken WF, Pajon A, Stevens TJ, Bhat TN, Westbrook J, Ionides JMC, and Laue ED.
2004 Proceedings of Second European Workshop on Model Driven Architecture (MDA) D. H. Akehurst (Ed.) Technical Report 17-04, University of Kent, Computing Laboratory. pp116–123.

The CCPN project: an interim report on a data model for the NMR community.
Fogh RH, Ionides J, Ulrich EL, Boucher W, Vranken WF, Linge JP, Habeck M, Rieping W, Bhat TN, Westbrook J, Henrick K, Gilliland G, Berman H, Thornton J, Nilges M, Markley J, and Laue E.
2002 Nature Structural Biology, 9(6), 416–418. view article

Collaboration to make the most of NMR.
BBSRC Business, July 2001