Related ArticlesProtein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
J Biomol NMR. 2013 Jun 2;
Authors: Shen Y, Bax A
Abstract
A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, >=90*% fraction of the residues, with an error rate smaller than ca 3.5*%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (?, ?) torsion angles of ca 12º. TALOS-N also reports sidechain ?(1) rotameric states for about 50*% of the residues, and a consistency with reference structures of 89*%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.
PMID: 23728592 [PubMed - as supplied by publisher]
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
Local protein backbone folds determined by calculated NMR chemical shifts.
J Comput Chem. 2011 Sep 9;
Authors: Czajlik A, Hudáky I, Perczel A
Abstract
NMR chemical shifts (CSs: ?N(NH) , ?C(?) , ?C(?) , ?C', ?H(NH) , and ?H(?) ) were computed for the amino acid backbone conformers (?(L) , ?(L) , ?(L) , ?(L) , ?(L) , ?(D) , ?(D) , ?(D) , and ?(D) ) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single ?-strands,...
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[NMR paper] Metabonomics classifies pathways affected by bioactive compounds. Artificial neural n
Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts.
Related Articles Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts.
Phytochemistry. 2003 Mar;62(6):971-85
Authors: Ott KH, Araníbar N, Singh B, Stockton GW
The biochemical mode-of-action (MOA) for herbicides and other bioactive compounds can be rapidly and simultaneously classified by automated pattern recognition of...
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[NMR paper] RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins
RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
Related Articles RESCUE: an artificial neural network tool for the NMR spectral assignment of proteins.
J Biomol NMR. 1999 Sep;15(1):15-26
Authors: Pons JL, Delsuc MA
The assignment of the 1H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1H...
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11-18-2010 08:31 PM
[NMR paper] Determination of multiple ***φ***-torsion angles in proteins by selective and ext
Determination of multiple ***φ***-torsion angles in proteins by selective and extensive (13)C labeling and two-dimensional solid-state NMR.
Related Articles Determination of multiple ***φ***-torsion angles in proteins by selective and extensive (13)C labeling and two-dimensional solid-state NMR.
J Magn Reson. 1999 Aug;139(2):389-401
Authors: Hong M
We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive (13)C labeling in conjunction with two-dimensional...
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[NMR paper] Using neural network predicted secondary structure information in automatic protein N
Using neural network predicted secondary structure information in automatic protein NMR assignment.
Related Articles Using neural network predicted secondary structure information in automatic protein NMR assignment.
J Chem Inf Comput Sci. 1997 Nov-Dec;37(6):1086-94
Authors: Choy WY, Sanctuary BC, Zhu G
In CAPRI, an automated NMR assignment software package that was developed in our laboratory, both chemical shift values and coupling topologies of spin patterns are used in a procedure for amino acids recognition. By using a knowledge base of...
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08-22-2010 05:08 PM
[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.
J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
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[NMR paper] Application of neural networks to automated assignment of NMR spectra of proteins.
Application of neural networks to automated assignment of NMR spectra of proteins.
Related Articles Application of neural networks to automated assignment of NMR spectra of proteins.
J Biomol NMR. 1994 Jan;4(1):35-46
Authors: Hare BJ, Prestegard JH
Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37%...
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[NMR paper] Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spi
Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants.
Related Articles Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants.
Biochemistry. 1991 Jan 29;30(4):986-96
Authors: Smith LJ, Sutcliffe MJ, Redfield C, Dobson CM
Three-bond 3JHN alpha coupling constants have been determined for 106 residues and 3J alpha beta coupling constants have been measured for 57 residues of the 129-residue protein hen egg white lysozyme. These NMR...
Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks.
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