Protein Structure Prediction from NMR Hydrogen–Deuterium Exchange Data

2021 ◽  
Vol 17 (4) ◽  
pp. 2619-2629
Author(s):  
Daniel R. Marzolf ◽  
Justin T. Seffernick ◽  
Steffen Lindert
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Exchange Data

New developments in protein structure-function analysis by MS and use of hydrogen-deuterium exchange microfluidics

FEBS Journal ◽  
2011 ◽  
Vol 278 (20) ◽  
pp. 3815-3821 ◽  
Author(s):  
Michael Landreh ◽  
Juan Astorga-Wells ◽  
Jan Johansson ◽  
Tomas Bergman ◽  
Hans Jörnvall
Keyword(s):  
Protein Structure ◽  
Structure Function ◽  
Function Analysis ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
New Developments ◽  
Hydrogen Deuterium

scholarly journals HD-eXplosion: visualization of hydrogen–deuterium exchange data as chiclet and volcano plots with statistical filtering

2020 ◽  
Author(s):  
Naifu Zhang ◽  
Xiaohe Yu ◽  
Xinchao Zhang ◽  
Sheena D’Arcy
Keyword(s):  
Source Code ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Web Based ◽  
Data Presentation ◽  
Software Packages ◽  
Volcano Plots ◽  
Hydrogen Deuterium ◽  
Exchange Data ◽  
Publication Quality

Abstract Summary Hydrogen–Deuterium eXchange coupled to mass spectrometry is a powerful tool for the analysis of protein dynamics and interactions. Bottom-up experiments looking at deuterium uptake differences between various conditions are the most common. These produce multi-dimensional data that can be challenging to depict in a single visual format. Each user must also set significance thresholds to define meaningful differences and make these apparent in data presentation. To assist in this process, we have created HD-eXplosion, an open-source, web-based application for the generation of chiclet and volcano plots with statistical filters. HD-eXplosion fills a void in available software packages and produces customizable plots that are publication quality. Availability and implementation The HD-eXplosion application is available at http://hd-explosion.utdallas.edu. The source code can be found at https://github.com/HD-Explosion.

Dual-spray hydrogen/deuterium exchange (HDX) reactions: A new method of probing protein structure

2016 ◽  
Vol 30 (13) ◽  
pp. 1505-1512 ◽  
Author(s):  
Shaan Rashid ◽  
Sean Overton ◽  
Bihac Mazigh ◽  
Paul M. Mayer
Keyword(s):  
Protein Structure ◽  
Deuterium Exchange ◽  
New Method ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium

scholarly journals Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability

2015 ◽  
Vol 44 (D1) ◽  
pp. D429-D434 ◽  
Author(s):  
Rita Pancsa ◽  
Mihaly Varadi ◽  
Peter Tompa ◽  
Wim F. Vranken
Keyword(s):  
Protein Folding ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Hydrogen Deuterium ◽  
Exchange Data

Hydrogen-deuterium exchange in membrane proteins monitored by IR spectroscopy: A new tool to resolve protein structure and dynamics

Biopolymers ◽  
2004 ◽  
Vol 74 (1-2) ◽  
pp. 19-26 ◽  
Author(s):  
C. Vigano ◽  
M. Smeyers ◽  
V. Raussens ◽  
F. Scheirlinckx ◽  
J.M. Ruysschaert ◽  
...  
Keyword(s):  
Protein Structure ◽  
Membrane Proteins ◽  
Ir Spectroscopy ◽  
Deuterium Exchange ◽  
Hydrogen Deuterium Exchange ◽  
Structure And Dynamics ◽  
Hydrogen Deuterium ◽  
Protein Structure And Dynamics
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