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NetTurnP specifications

Information


Unique identifier OMICS_17954
Name NetTurnP
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Thomas Nordahl Petersen

Publication for NetTurnP

NetTurnP citations

 (9)
library_books

ACTH Receptor (MC2R) Specificity: What Do We Know About Underlying Molecular Mechanisms?

2017
PMCID: 5292628
PMID: 28220105
DOI: 10.3389/fendo.2017.00013

[…] extracellular region of MCRs (, , ). It is presumed that in the case of ACTHR these are formed between C245 and C251, and between C21 and C253 (Figure ). Both the MC4R model and predictions using the NetTurnP 1.0 server () indicate that the bond between this first pair of residues “locks” the conserved –P–Q–N–P–Y– motif of extracellular loop (EL) 3 into a β-turn-like structure, thus exposing its N […]

library_books

Longipin: An Amyloid Antimicrobial Peptide from the Harvestman Acutisoma longipes (Arachnida: Opiliones) with Preferential Affinity for Anionic Vesicles

2016
PLoS One
PMCID: 5172563
PMID: 27997568
DOI: 10.1371/journal.pone.0167953

[…] ed but also presented a high β-turn content, which is in agreement with the presence of Pro-Gly motif in the primary structure, that would favor formation of a type II β-turn. Moreover, prediction by NetTurnP method [] pointed to the presence of a β-turn in the segment Leu4-Pro5-Gly6-Lys7, which corresponds to 22% of the peptide chain. In quantitative agreement with this result, FT-IR spectrum of […]

library_books

Evidence for the recent origin of a bacterial protein coding, overlapping orphan gene by evolutionary overprinting

2015
BMC Evol Biol
PMCID: 4683798
PMID: 26677845
DOI: 10.1186/s12862-015-0558-z

[…] t 86 % accuracy []. Finally, BCL::Jufo9D has a prediction accuracies of 73.2 % the secondary structure prediction, and 94.8 % for the transmembrane span prediction []. Beta-turns were predicted using NetTurnP []. Sensitivity is 76 % and specificity 79 %, respectively, in distinguishing turns from not-turns []. The protein secondary structure was established using SOPMA [], PSIPRED [], Pred2ary [], […]

library_books

TECPR2 Associated Neuroaxonal Dystrophy in Spanish Water Dogs

2015
PLoS One
PMCID: 4640708
PMID: 26555167
DOI: 10.1371/journal.pone.0141824

[…] available from UniProtKB/Swiss-Prot: Q9VWB0.2 (Drosophila melanogaster). Impact of the mutations on the protein stability and structure was predicted with the following software tools: PolyPhen2 [], NetTurnP [], NetSurfP [], the Chou&Fasman secondary structure prediction server CFSSP [], PoPMuSiC [], and Phyre2 []. […]

library_books

Predicting beta turns in proteins using support vector machines with fractional polynomials

2013
Proteome Sci
PMCID: 3908855
PMID: 24565438
DOI: 10.1186/1477-5956-11-S1-S5

[…] and Kurgan's method and the method of Liu et al. provide 5.9/25 = 24% error rate reduction, and Hu and Li's method provides 4.8/25 = 19% error rate reduction.H-SVM-LR shows high MCC 0.56 compared to NetTurnP 0.50, Zheng and Kurgan's method 0.47, and the method of Liu et al. 0.44. Thus, H-SVM-LR has the highest MCC and Qtotal among the other β-turns prediction methods. The MCC value achieved is no […]

library_books

Turn Directed α β Conformational Transition of α syn12 Peptide at Different pH Revealed by Unbiased Molecular Dynamics Simulations

2013
Int J Mol Sci
PMCID: 3709708
PMID: 23708094
DOI: 10.3390/ijms140610896

[…] at physiological pH than acidic pH.Residues such as Asn, Asp, Gly, Pro and Ser tend to form turns. In this sequence, the probabilities of each residue to form turns can be predicted with the software NetTurnP [] and the results are shown in . At physiological pH, Asp2 is negatively charged, which experiences electrostatic attraction from Lys6. However, at acidic pH, Asp2 is neutral. This makes it […]


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NetTurnP institution(s)
Department of Systems Biology, Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Lyngby, Denmark

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