Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data

Abstract

We present Farseer-NMR (https://git.io/vAueU), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution. These advances have created a growing need to analyse those systems’ responses to multiple variables. The combined analysis of NMR peaklists from large and multivariable datasets has become a new bottleneck in the NMR analysis pipeline, whereby information-rich NMR-derived parameters have to be manually generated, which can be tedious, repetitive and prone to human error, or even unfeasible for very large datasets. There is a persistent gap in the development and distribution of software focused on peaklist treatment, analysis and representation, and specifically able to handle large multivariable datasets, which are becoming more commonplace. In this regard, Farseer-NMR aims to close this longstanding gap in the automated NMR user pipeline and, altogether, reduce the time burden of analysis of large sets of peaklists from days/weeks to seconds/minutes. We have implemented some of the most common, as well as new, routines for calculation of NMR parameters and several publication-quality plotting templates to improve NMR data representation. Farseer-NMR has been written entirely in Python and its modular code base enables facile extension.Electronic supplementary materialThe online version of this article (10.1007/s10858-018-0182-5) contains supplementary material, which is available to authorized users.

The Two Isoforms of Lyn Display Different Intramolecular Fuzzy Complexes with the SH3 Domain

“…Peaklist datasets were exported from CcpNmr [ 28 ] and analyzed with Farseer-NMR [ 29 ] to generate the Chemical shift perturbations and PRE profiles and respective plots. Combined chemical shift differences were calculated using the following equation: where α is 0.14, but 0.2 for Gly [ 30 ].…”

“…Other software for data representation and figure preparation . Figures were prepared combining the output from Farseer-NMR [ 29 ], UCSF Chimera [ 32 ] and GIMP (GNU Image Manipulation Program).…”

Integrating disorder in globular multidomain proteins: Fuzzy sensors and the role of SH3 domains

“…Interestingly, the SH3 regions in contact with the disordered domains correspond to the flexible loops suggesting that the SH3 domain share characteristics of folded domains and disordered regions. Paramagnetic relaxation enhancements within the disordered regions were analyzed as ΔPRE, to emphasize departures from a random coil model [39]. The ΔPRE pattern confirms transient contacts within the Unique domain that are retained in the isolated and SH3 bound forms.…”

Intramolecular Fuzzy Interactions Involving Intrinsically Disordered Domains

“…The ΔPRE method is a simple and robust analytical approach to generate a fingerprint of the long-range interactions within intrinsically disordered domains. The complete processing tools are part of the Farseer software (Teixeira et al, in press ).…”