CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis.
NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.
Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK.
Simon P
SP
Skinner
Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK.
Rasmus H
RH
Fogh
Department of Biochemistry, University of Cambridge, Cambridge, UK.
Wayne
W
Boucher
Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK.
Timothy J
TJ
Ragan
Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK.
Luca G
LG
Mureddu
Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology, University of Leicester, Leicester, UK. gv29@le.ac.uk.
Geerten W
0000-0001-6172-5097
GW
Vuister
D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D012984:Software; D013223:Statistics as Topic; D014584:User-Computer Interface; D057188:Workflow
Assignment; CCPN; Data analysis; NMR; Python; Software
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii230-6
16204110
J Biomol NMR. 1995 Jul;6(1):1-10
22911575
J Biomol NMR. 1995 Nov;6(3):277-93
8520220
J Mol Biol. 1997 Jun 20;269(4):592-610
9217263
J Am Chem Soc. 2005 Aug 31;127(34):11920-1
16117513
J Biomol NMR. 2004 Sep;30(1):11-23
15452431
Nat Struct Mol Biol. 2015 Jun;22(6):433-4
26036565
J Biomol NMR. 1994 Sep;4(5):603-14
22911360
J Am Chem Soc. 2006 Oct 11;128(40):13112-22
17017791
Nat Protoc. 2010 Jun;5(6):1051-60
20539281
Nat Chem Biol. 2009 Nov;5(11):808-14
19841630
Proc Natl Acad Sci U S A. 2002 May 14;99(10):6707-12
12011433
Proteins. 2005 Jun 1;59(4):687-96
15815974
Q Rev Biophys. 2015 Feb;48(1):35-116
25710841
PLoS Comput Biol. 2009 Mar;5(3):e1000307
19282963
J Integr Bioinform. 2010 Mar 25;7(3):null
20375445