Related ArticlesRapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS.
Methods Mol Biol. 2018;1688:111-132
Authors: Narasimhan S, Mance D, Pinto C, Weingarth M, Bonvin AMJJ, Baldus M
Abstract
Solid-state NMR (ssNMR) can provide structural information at the most detailed level and, at the same time, is applicable in highly heterogeneous and complex molecular environments. In the last few years, ssNMR has made significant progress in uncovering structure and dynamics of proteins in their native cellular environments [1-4]. Additionally, ssNMR has proven to be useful in studying large biomolecular complexes as well as membrane proteins at the atomic level [5]. In such studies, innovative labeling schemes have become a powerful approach to tackle spectral crowding. In fact, selecting the appropriate isotope-labeling schemes and a careful choice of the ssNMR experiments to be conducted are critical for applications of ssNMR in complex biomolecular systems. Previously, we have introduced a software tool called FANDAS (Fast Analysis of multidimensional NMR DAta Sets) that supports such investigations from the early stages of sample preparation to the final data analysis [6]. Here, we present a new version of FANDAS, called FANDAS 2.0, with improved user interface and extended labeling scheme options allowing the user to rapidly predict and analyze ssNMR data sets for a given protein-based application. It provides flexible options for advanced users to customize the program for tailored applications. In addition, the list of ssNMR experiments that can be predicted now includes proton ((1)H) detected pulse sequences. FANDAS 2.0, written in Python, is freely available through a user-friendly web interface at http://milou.science.uu.nl/services/FANDAS .
[NMR paper] Using Complementary NMR Data Sets to Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4.
Using Complementary NMR Data Sets to Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4.
Related Articles Using Complementary NMR Data Sets to Detect Inconsistencies and Model Flaws in the Structure Determination of Human Interleukin-4.
J Phys Chem B. 2017 Jun 22;:
Authors: Smith LJ, van Gunsteren WF, Hansen N
Abstract
The derivation of protein structure from values of observable quantities measured in NMR experiments is a rather non-trivial task due to (i) the limited number of data...
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06-24-2017 08:20 PM
[NMR paper] Fast multi-dimensional NMR acquisition and processing using the sparse FFT.
Fast multi-dimensional NMR acquisition and processing using the sparse FFT.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Fast multi-dimensional NMR acquisition and processing using the sparse FFT.
J Biomol NMR. 2015 Sep;63(1):9-19
Authors: Hassanieh H, Mayzel M, Shi L, Katabi D, Orekhov VY
Abstract
Increasing the dimensionality of NMR experiments strongly enhances the spectral resolution and provides invaluable direct...
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06-21-2016 01:30 PM
[NMR paper] Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
J Biomol NMR. 2013 Aug 14;
Authors: Bellstedt P, Seiboth T, Häfner S, Kutscha H, Ramachandran R, Görlach M
Abstract
NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though...
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08-15-2013 07:45 PM
[NMR paper] Rapid prediction of multi-dimensional NMR data sets.
Rapid prediction of multi-dimensional NMR data sets.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Rapid prediction of multi-dimensional NMR data sets.
J Biomol NMR. 2012 Dec;54(4):377-87
Authors: Gradmann S, Ader C, Heinrich I, Nand D, Dittmann M, Cukkemane A, van Dijk M, Bonvin AM, Engelhard M, Baldus M
Abstract
We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling...
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05-15-2013 03:12 PM
Rapid prediction of multi-dimensional NMR data sets
Rapid prediction of multi-dimensional NMR data sets
Abstract We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such â??in silicoâ?? data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of...
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11-14-2012 08:07 AM
[Question from NMRWiki Q&A forum] transfer of data sets/pulse sequences from Xwinnmr/DRX to Avance III/topspin
transfer of data sets/pulse sequences from Xwinnmr/DRX to Avance III/topspin
How do I transfer data sets ( with pulse sequences for measurements of various cross- -relaxtion rates) collected under Xwinnmr DRX console to an Avance III console with topspin 3. (on the same instrument/probe). Is it a straigtforward copying of the data folders, or are there any caveats involved? thank you for any input
Check if somebody has answered this question on NMRWiki QA forum
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03-06-2011 03:29 AM
[NMR paper] Fast multi-dimensional NMR of proteins.
Fast multi-dimensional NMR of proteins.
Related Articles Fast multi-dimensional NMR of proteins.
J Biomol NMR. 2003 Apr;25(4):349-54
Authors: Kupce E, Freeman R
Three-dimensional HNCO and HNCA subspectra from a small protein (agitoxin, 4 kDa, enriched in carbon-13 and nitrogen-15), have been obtained by direct frequency-domain excitation of selected carbon and nitrogen sites. This new technique applies an array of several simultaneous soft radiofrequency spin-inversion pulses, encoded (on or off) according to nested Hadamard matrices, and the...
Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS.
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