CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis

Abstract

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.

Simple high‐resolution NMR spectroscopy as a tool in molecular biology

“…According to Lee and Markley, based on BMRB statistics in 2014, Sparky was still the most widely used NMR data analysis tool for backbone assignment [7]. A much more recent programme, not included in their list, is CcpNmr AnalysisAssign version-3 [8], which provides tools for simple and semi-automated backbone assignments and a dedicated interactive CSP analysis module, from here on referred to as the CSP module ( Fig. 2C).…”

“…Importantly, to ensure a valid analysis all spectra should be properly referenced as changes in peak positions could otherwise be misinterpreted. Fortunately, AnalysisAssign has routines to establish, and where needed report, on the spectral alignment that functions even in the case of non-fully identical spectra [8]. Using an automated analysis, in which all the peaks were accurately matched to their extrema, CSP i values are calculated for each Tstar-KH residue i using Eqn (2) and displayed automatically as a bar plot in the CSP module interface.…”

Structure, dynamics and roX2-lncRNA binding of tandem double-stranded RNA binding domains dsRBD1,2 of Drosophila helicase Maleless

“…For structure determination data were recorded with 0.8 mM protein in 20 mM sodium phosphate (pH 6.5), 200 mM NaCl and 1 mM DTT with 10% D2O added for the deuterium lock. All spectra were processed using NMRPipe (27) and analysed using CCPNmr (28). Protein backbone assignments were obtained from HNCO, HNCA, CBCA(CO)NH, HNCACB (29) and HBHA(CO)NH (30) experiments.…”

“…Titrations for the single domains, 0.05 mM dsRBD1 wt or mutants or 0.1 mM dsRBD2 were titrated with 18-mer double stranded roX-box RNA derived from SL7 respectively. Data analysis for calculating chemical shift perturbations and dissociation constants were performed with the CCPN analysis software (28).…”

Beyond Fourier

“…Because so many modern methods lack formal mathematical descriptions, empirical critical comparisons are the only way to establish best practices, making it doubly important that software developers make available the complete software environment – including codes, data, and meta-data – that is required to reproduce their results. Resources such as the public data repository BMRB [61] and the NMR software platforms CCPN [62, 63], WeNMR [64], SBGrid [65], and NMRbox [66] facilitate these comparisons, but it is incumbent upon journals, funding agencies, and the NMR community to ensure that published studies meet basic reporting and reproducibility standards.…”