Protein secondary structure provides rich structural information, hence the description and understanding of protein structure relies heavily on it. Identification or prediction of secondary structures therefore plays an important role in protein research. In protein NMR studies, it is more convenient to predict secondary structures from chemical shifts as compared to the traditional determination methods based on inter-nuclear distances provided by NOESY experiment. In recent years, there was a significant improvement observed in deep neural networks, which had been applied in many research fields. Here we proposed a deep neural network based on bidirectional long short term memory (biLSTM) to predict protein 3-state secondary structure using NMR chemical shifts of backbone nuclei. While comparing with the existing methods the proposed method showed better prediction accuracy. Based on the proposed method, a web server has been built to provide protein secondary structure prediction service.
[NMR paper] A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory.
A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory.
A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory.
J Comput Chem. 2016 Mar 4;
Authors: Shaghaghi H, Ebrahimi HP, Fathi F, Bahrami Panah N, Jalali-Heravi M, Tafazzoli M
Abstract
The dependency of amino acid chemical shifts on ? and ? torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF)...
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03-05-2016 11:21 AM
[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] 1H NMR study on the short- and long-term impact of two training programs of sprint running on the metabolic fingerprint of human serum.
1H NMR study on the short- and long-term impact of two training programs of sprint running on the metabolic fingerprint of human serum.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles 1H NMR study on the short- and long-term impact of two training programs of sprint running on the metabolic fingerprint of human serum.
J Proteome Res. 2013 Jan 4;12(1):470-80
Authors: Pechlivanis A, Kostidis S, Saraslanidis P, Petridou A, Tsalis G, Veselkov K, Mikros E, Mougios V, Theodoridis GA...
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06-08-2013 02:18 PM
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts.
Related Articles Secondary structural effects on protein NMR chemical shifts.
J Biomol NMR. 2004 Nov;30(3):233-44
Authors: Wang Y
For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
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11-24-2010 10:03 PM
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecu
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules.
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules.
J Phys Chem B. 2010 Nov 18;
Authors: Atieh Z, Aubert-Fre?con M, Allouche AR
We present a new model to predict chemical shifts for biological molecules. It is simple, fast, and involves a limited number of parameters. It is particularly adapted to be used in molecular dynamics studies with a molecular mechanic potential. We test the model for polyamines, which are rather...
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11-20-2010 06:01 PM
[NMR paper] 13C NMR chemical shifts can predict disulfide bond formation.
13C NMR chemical shifts can predict disulfide bond formation.
Related Articles 13C NMR chemical shifts can predict disulfide bond formation.
J Biomol NMR. 2000 Oct;18(2):165-71
Authors: Sharma D, Rajarathnam K
The presence of disulfide bonds can be detected unambiguously only by X-ray crystallography, and otherwise must be inferred by chemical methods. In this study we demonstrate that 13C NMR chemical shifts are diagnostic of disulfide bond formation, and can discriminate between cysteine in the reduced (free) and oxidized (disulfide bonded)...
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11-19-2010 08:29 PM
PECAN server - protein secondary structure via NMR
http://bija.nmrfam.wisc.edu/PECAN/Pecan.jpg
Link to the PECAN server
Instructions about PECAN input files
Info from the PECAN website:PECAN offers a new approach to secondary structure identification that achieves excellent results.
PECAN is a component in a suite of tools for high-throughput structure determination using NMR.
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07-20-2005 05:44 PM
PSSI: secondary structure from chemical shifts
Link to PSSI program
Reference and abstract:
Probability-based protein secondary structure identification using combined NMR chemical-shift data.
Wang Y, Jardetzky O.
Division of Chemical Biology, Department of Molecular Pharmacology, Stanford University, Stanford, California 94305, USA.
CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts
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