scholarly journals Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum

2013 ◽  
Vol 8 (1) ◽  
pp. 177-179 ◽  
Author(s):  
Benjamin G. Bobay ◽  
Richele J. Thompson ◽  
Debra L. Milton ◽  
John Cavanagh
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Vibrio Anguillarum ◽  
Chemical Shift Assignments

Chemical shift assignments and secondary structure prediction for Q4DY78, a conserved kinetoplastid-specific protein from Trypanosoma cruzi

2016 ◽  
Vol 10 (2) ◽  
pp. 325-328
Author(s):  
Éverton Dias D’Andréa ◽  
Anne Diehl ◽  
Peter Schmieder ◽  
Hartmut Oschkinat ◽  
José Ricardo Pires
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Trypanosoma Cruzi ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Specific Protein ◽  
Chemical Shift Assignments

scholarly journals Chemical shift assignments and secondary structure prediction of the master biofilm regulator, SinR, from Bacillus subtilis

2013 ◽  
Vol 8 (1) ◽  
pp. 155-158 ◽  
Author(s):  
Sean D. Stowe ◽  
Andrew L. Olson ◽  
Richard Losick ◽  
John Cavanagh
Keyword(s):  
Bacillus Subtilis ◽  
Chemical Shift ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Chemical Shift Assignments

PROTEIN SECONDARY STRUCTURE PREDICTION USING NMR CHEMICAL SHIFT DATA

2010 ◽  
Vol 08 (05) ◽  
pp. 867-884 ◽  
Author(s):  
YUZHONG ZHAO ◽  
BABAK ALIPANAHI ◽  
SHUAI CHENG LI ◽  
MING LI
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Nearest Neighbor ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Accurate Determination ◽  
Protein Secondary Structure ◽  
Sequence Information ◽  
K Nearest Neighbor

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q3 accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at .

scholarly journals Enhanced Chemical Shift Analysis for Secondary Structure prediction of protein

2014 ◽  
Vol 18 (1) ◽  
pp. 36-40 ◽  
Author(s):  
Won-Je Kim ◽  
Jin-Kyu Rhee ◽  
Jong-Jae Yi ◽  
Bong-Jin Lee ◽  
Woo Sung Son
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Shift Analysis ◽  
Chemical Shift Analysis

Chemical shift dispersion and secondary structure prediction in unfolded and partly folded proteins

FEBS Letters ◽  
1997 ◽  
Vol 419 (2-3) ◽  
pp. 285-289 ◽  
Author(s):  
Jian Yao ◽  
H.Jane Dyson ◽  
Peter E Wright
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Folded Proteins
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