Abstract
Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino acid residue, chemical shifts present multi-dimensional and complexly cross-correlated information, making them difficult to analyse. The ShiftCrypt method, based on neural network auto-encoder architecture, compresses the per-amino acid chemical shift information in a single, interpretable, amino acid-type independent value that reflects the biophysical state of a residue. We here present the ShiftCrypt web server, which makes the method readily available. The server accepts chemical shifts input files in the NMR Exchange Format (NEF) or NMR-STAR format, executes ShiftCrypt and visualises the results, which are also accessible via an API. It also enables the "biophysically-based" pairwise alignment of two proteins based on their ShiftCrypt values. This approach uses Dynamic Time Warping and can optionally include their amino acid code information, and has applications in, for example, the alignment of disordered regions. The server uses a token-based system to ensure the anonymity of the users and results. The web server is available at www.bio2byte.be/shiftcrypt.
PMID: 32459331 [PubMed - as supplied by publisher]
Rapid automated determination of chemical shift anisotropy values in the carbonyl and carboxyl groups of fd-y21m bacteriophage using solid state NMR
Rapid automated determination of chemical shift anisotropy values in the carbonyl and carboxyl groups of fd-y21m bacteriophage using solid state NMR
Abstract
Determination of chemical shift anisotropy (CSA) in immobilized proteins and protein assemblies is one of several tools to determine protein dynamics on the timescales of microseconds and faster. The large CSA values of C=O groups in the rigid limit makes them in particular attractive for measurements of large amplitude motions, or their absence. In this study, we implement a 3D...
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11-25-2018 06:02 AM
The PROSECCO server for chemical shift predictions in ordered and disordered proteins
The PROSECCO server for chemical shift predictions in ordered and disordered proteins
Abstract
The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences....
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11-09-2017 08:55 AM
[NMR paper] The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.
The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.
Related Articles The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.
Angew Chem Int Ed Engl. 2016 Jun 10;
Authors: Frach R, Kibies P, Böttcher S, Pongratz T, Strohfeldt S, Kurrmann S, Koehler J, Hofmann M, Kremer W, Kalbitzer HR, Reiser O, Horinek D, Kast SM
Abstract
High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for...
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06-11-2016 01:09 PM
[NMR paper] CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.
CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.
Related Articles CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.
Nucleic Acids Res. 2015 May 15;
Authors: Hafsa NE, Arndt D, Wishart DS
Abstract
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only...
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05-17-2015 03:52 PM
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
J Biomol NMR. 2013 Apr 28;
Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M
Abstract
We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
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04-30-2013 10:21 PM
Calculation of chemical shift anisotropy in proteins
Calculation of chemical shift anisotropy in proteins
Abstract Individual peptide groups in proteins must exhibit some variation in the chemical shift anisotropy (CSA) of their constituent atoms, but not much is known about the extent or origins of this dispersion. Direct spectroscopic measurement of CSA remains technically challenging, and theoretical methods can help to overcome these limitations by estimating shielding tensors for arbitrary structures. Here we use an automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach to compute 15N, 13Câ?² and 1H...
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08-29-2011 06:41 AM
[NMR paper] Proline-directed random-coil chemical shift values as a tool for the NMR assignment o
Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites.
Related Articles Proline-directed random-coil chemical shift values as a tool for the NMR assignment of the tau phosphorylation sites.
Chembiochem. 2004 Jan 3;5(1):73-8
Authors: Lippens G, Wieruszeski JM, Leroy A, Smet C, Sillen A, Buée L, Landrieu I
NMR spectroscopy of the full-length neuronal Tau protein has proved to be difficult due to the length of the protein and the unfavorable amino acid composition. We show that the...
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values.
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