Related ArticlesFarseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data.
J Biomol NMR. 2018 May 11;:
Authors: Teixeira JMC, Skinner SP, Arbesú M, Breeze AL, Pons M
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.
PMID: 29752607 [PubMed - as supplied by publisher]
Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data
Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data
Abstract
We present Farseer-NMRÂ*(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....
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05-12-2018 02:10 AM
Automatic methyl assignment in large proteins by the MAGIC algorithm
Automatic methyl assignment in large proteins by the MAGIC algorithm
Abstract
Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein....
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11-03-2017 04:15 AM
Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data
Automatic Protein Structure Determination from Sparse NMR Spectroscopy Data
Publication date: 16 February 2016
Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br>
Author(s): Justin L. MacCallum, Yuefeng Tang, Y. Janet Huang, Gaetano T. Montelione</br>
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02-17-2016 07:50 PM
[NMR paper] [FTIR and 13C NMR Analysis of Dissolved Organic Matter (DOM) in the Treatment Process of Tannery Wastewater].
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Related Articles .
Guang Pu Xue Yu Guang Pu Fen Xi. 2015 May;35(5):1203-7
Authors: Fan CH, Zhang YC, Tang ZH, Wang JH
Abstract
Nowadays, the wastewater quantity discharged yearly from tannery industry is around 0. 2 billion t in China. The contaminants of tannery wastewater include macromolecular organic matters, such as grease, fur scraps and collagen, and the alkaline wastewater appears to be of high content of salt and COD. The quality of tannery wastewater is monitored strictly among all kinds of industry wastewater....
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09-30-2015 10:34 PM
[NMR paper] Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data.
Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data.
Related Articles Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data.
J Biomol NMR. 2014 Sep 6;
Authors: Xiang S, Chevelkov V, Becker S, Lange A
Abstract
We introduce an efficient approach for sequential protein backbone assignment based on two complementary proton-detected 4D solid-state NMR experiments that correlate /Ni with CAi/COi or CAi-1/COi-1. The resulting 4D spectra exhibit excellent...
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09-07-2014 12:36 PM
Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data
Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data
Abstract
We introduce an efficient approach for sequential protein backbone assignment based on two complementary proton-detected 4D solid-state NMR experiments that correlate \( {\text{H}}_{{\text{i}}}^{{\text{N}}} \) /Ni with CAi/COi or CAiâ??1/COiâ??1. The resulting 4D spectra exhibit excellent sensitivity and resolution and are amenable to (semi-)automatic assignment...
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09-06-2014 07:41 AM
Multi-dimensional NMR without coherence transfer: Minimizing losses in large systems.
Multi-dimensional NMR without coherence transfer: Minimizing losses in large systems.
Multi-dimensional NMR without coherence transfer: Minimizing losses in large systems.
J Magn Reson. 2011 Jul 21;
Authors: Liu Y, Prestegard JH
Most multi-dimensional solution NMR experiments connect one dimension to another using coherence transfer steps that involve evolution under scalar couplings. While experiments of this type have been a boon to biomolecular NMR the need to work on ever larger systems pushes the limits of these procedures. Spin relaxation...
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08-13-2011 12:57 PM
SAGA: rapid automatic mainchain NMR assignment for large proteins
Abstract Here we describe a new algorithm for automatically determining the mainchain sequential assignment of NMR spectra for proteins. Using only the customary triple resonance experiments, assignments can be quickly found for not only small proteins having rather complete data, but also for large proteins, even when only half the residues can be assigned. The result of the calculation is not the single best assignment according to some criterion, but rather a large number of satisfactory assignments that are summarized in such a way as to help the user identify portions of the sequence...
Farseer-NMR: automatic treatment, analysis and plotting of large, multi-variable NMR data.
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