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NORSp: predictions of long regions without regular secondary structure
2003
Nucleic Acids Research
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Here, we present NORSp, a publicly available predictor for disordered regions in protein. Specifically, NORSp predicts long regions with NO Regular Secondary structure. ...
Upon user submission of a protein sequence, NORSp will analyse the protein for its secondary structure, presence of transmembrane helices and coiled-coil. ...
This work was supported by grants 1-P50-GM62413-01 and RO1-GM63029-01 from the National Institute of Health (NIH). ...
doi:10.1093/nar/gkg515
pmid:12824431
pmcid:PMC168922
fatcat:7uwce7tlaragjmag6xaefy7i2e
The PredictProtein server
2004
Nucleic Acids Research
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structure (NORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular localization ...
PredictProtein (http://www.predictprotein.org) is an Internet service for sequence analysis and the prediction of protein structure and function. ...
ACKNOWLEDGEMENTS Making PredictProtein survive a decade was a major effort; many colleagues helped with hands and brains; thanks to all of them! ...
doi:10.1093/nar/gkh377
pmid:15215403
pmcid:PMC441515
fatcat:ohufej34lzd4zajpydx25i6rmq
Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle
2007
Nature Precedings
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It was inferred that the global structure of SV-IV is not similar to any protein of known three-dimensional structure. ...
More structural details that integrate experimental data into a predictive framework have recently been reported. ...
NORSp is an on-line predictor of NOn-Regular Secondary Structure (NORS) that is not trained on any dataset and predicts segments in which the content in regular secondary structure is below 12% over at ...
doi:10.1038/npre.2007.1394.1
fatcat:yjrlypfv5fd2bfwaoutadmqale
Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle
2008
The FEBS Journal
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It was inferred that the global structure of SV-IV is not similar to any protein of known three-dimensional structure. ...
More structural details that integrate experimental data into a predictive framework have recently been reported. ...
NORSp is an on-line predictor of NOn-Regular Secondary Structure (NORS) that is not trained on any dataset and predicts segments in which the content in regular secondary structure is below 12% over at ...
doi:10.1111/j.1742-4658.2007.06242.x
pmid:18215165
fatcat:ylc3kupghrccnlzlncxnbzrzgq
Natively Unstructured Loops Differ from Other Loops
2005
PLoS Computational Biology
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We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features ...
Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. ...
The work was supported by grants U54-GM074958-01 from the Protein Structure Initiative of the US National Institutes of Health to the Northeast Structural Genomics Consortium and 2R01-LM07329-01 from the ...
doi:10.1371/journal.pcbi.0030140.eor
fatcat:5r4bwlgegjfqplmc36oobheroy
Natively Unstructured Loops Differ from Other Loops
2007
PLoS Computational Biology
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We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features ...
Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. ...
The work was supported by grants U54-GM074958-01 from the Protein Structure Initiative of the US National Institutes of Health to the Northeast Structural Genomics Consortium and 2R01-LM07329-01 from the ...
doi:10.1371/journal.pcbi.0030140
pmid:17658943
pmcid:PMC1924875
fatcat:zxnjdv65fbhl7cwtbv5nvp4qhe
Protein Disorder Prediction
2003
Structure
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In contrast, the nonglobular sub-D-69117 Heidelberg Germany space encompasses disordered, unstructured and flexible regions without regular secondary structure. ...
Globular units are built of regular secondary structure 3 CellZome GmbH Meyerhofstr 1 elements and contribute the majority of the structural data deposited in PDB. ...
Regions without regular secondary strucsolved on truncated polypeptides explicitly because the ture can be predicted by the NORSp (Non Regular Strucparts that are cut off are disordered or highly flexible ...
doi:10.1016/j.str.2003.10.002
pmid:14604535
fatcat:wqoqz5cvgvfnthpyw7x6varca4
PredictProtein—an open resource for online prediction of protein structural and functional features
2014
Nucleic Acids Research
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Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil ...
PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. ...
NORSnet (22) predicts disordered regions with NO Regular Secondary structure (NORS (46), i.e. long loops), separating very long disordered loops predicted by NORSp (47) from all other regions in the ...
doi:10.1093/nar/gku366
pmid:24799431
pmcid:PMC4086098
fatcat:c5pmgwyx7zg4jjncj4eywixmf4
OPTIMIZING LONG INTRINSIC DISORDER PREDICTORS WITH PROTEIN EVOLUTIONARY INFORMATION
2005
Journal of Bioinformatics and Computational Biology
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Here we focus on improving sequence-based predictions of long (> 30 amino acid residues) regions lacking specific 3-D structure by means of four new neural -network-based Predictors Of Natural Disordered ...
Protein existing as an ensemble of structures, called intrinsically disordered, has been shown to be res ponsible for a wide variety of biological functions and to be common in nature. ...
We also thank Vladimir Vacic for the construction of disorder database and predictor website. ...
doi:10.1142/s0219720005000886
pmid:15751111
fatcat:ndeogl654rcvxhvntke52hlfvi
A comprehensive overview of computational protein disorder prediction methods
2012
Molecular Biosystems
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Recognition of disordered regions in a protein is of great importance for protein structure prediction, protein structure determination and function annotation as these regions have a close relationship ...
Disordered regions are segments of the protein chain which do not adopt a stable structure. ...
Acknowledgments We thank Zheng Wang for his help with data preparation used in the evaluation of disorder predictions. The work was partially supported by a NIH grant (1R01GM093123) to JC. ...
doi:10.1039/c1mb05207a
pmid:21874190
pmcid:PMC3633217
fatcat:l6g4ebp3hzhljgk7qqcehvvz2m
Performance of Protein Disorder Prediction Programs on Amino Acid Substitutions
2014
Human Mutation
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without other information indicating to the relevance of disorder. ...
Prediction programs have been developed to detect disordered regions from sequences and used to predict the consequences of variants, although, their performance for this task has not been assessed. ...
Disclosure statement: The authors declare no conflict of interest. ...
doi:10.1002/humu.22564
pmid:24753228
fatcat:s6g5jskqn5cefob7m7ga2h5goi
Ebola Virus VP30 Is an RNA Binding Protein
2007
Journal of Virology
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VP30 acts in trans with an RNA secondary structure upstream of the first transcriptional start site to modulate transcription. ...
Enhancement of transcription by VP30 requires a RNA stem-loop located within nucleotides 54 to 80 of the leader region. ...
upon binding to RNA without, however, gaining any regular secondary structure elements. ...
doi:10.1128/jvi.02523-06
pmid:17567691
pmcid:PMC1951390
fatcat:45dhgnjxjvbmpbr6wif464iyai
Intrinsic Disorder and Functional Proteomics
2007
Biophysical Journal
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Next, the major statistical properties of disordered regions are summarized, and prediction models developed thus far are described, including their numerous applications in functional proteomics. ...
The future of the prediction of protein disorder and the future uses of such predictions in functional proteomics comprise the last section of this article. ...
Indeed, NORS stands for NOn-Regular secondary Structure. ...
doi:10.1529/biophysj.106.094045
pmid:17158572
pmcid:PMC1796814
fatcat:jl4rcmcnh5bdxegic5cy6deoia
How disordered is my protein and what is its disorder for? A guide through the "dark side" of the protein universe
2016
Intrinsically Disordered Proteins
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The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to structural determination with X-ray ...
This article discusses a comprehensive selection of databases and methods currently employed to disseminate experimental and putative annotations of disorder, predict disorder and identify regions involved ...
, since the others only predict regions lacking regular secondary structure. ...
doi:10.1080/21690707.2016.1259708
pmid:28232901
pmcid:PMC5314888
fatcat:zetixzpkyvhntjv4pkwmrfu5ee
N-terminal Domains of DELLA Proteins Are Intrinsically Unstructured in the Absence of Interaction with GID1/Gibberellic Acid Receptors
2010
Journal of Biological Chemistry
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However, the conformational changes of DELLAs upon binding to GID1/GA, which are the key to understanding the precise mechanism of GID1/GA-mediated degradation of DELLAs, remain unclear. ...
Binding of the liganded GA receptor (GID1/GA) to the N-terminal domain of DELLAs is required for GA-induced degradation of DELLAs via the ubiquitin-proteasome pathway, thus derepressing plant growth. ...
An independent predictor of non-regular secondary structure (NORSp) that adopts different definitions of disorder to distinguish unstructured loop regions from regular structured loops was also used to ...
doi:10.1074/jbc.m109.027011
pmid:20103592
pmcid:PMC2857034
fatcat:5ucnadzjtbbw5a5257gqjdyhua
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