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NORSp: predictions of long regions without regular secondary structure

J. Liu
2003 Nucleic Acids Research  
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

B. Rost, G. Yachdav, J. Liu
2004 Nucleic Acids Research  
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

Silvia Vilasi, Raffaele Ragone
2007 Nature Precedings  
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

Silvia Vilasi, Raffaele Ragone
2008 The FEBS Journal  
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

Avner Schlessinger, Jinfeng Liu, Burkhard Rost
2005 PLoS Computational Biology  
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

Avner Schlessinger, Jinfeng Liu, Burkhard Rost
2007 PLoS Computational Biology  
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

Rune Linding, Lars Juhl Jensen, Francesca Diella, Peer Bork, Toby J Gibson, Robert B Russell
2003 Structure  
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

Guy Yachdav, Edda Kloppmann, Laszlo Kajan, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, Lothar Richter, Haim Ashkenazy (+8 others)
2014 Nucleic Acids Research  
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

KANG PENG, SLOBODAN VUCETIC, PREDRAG RADIVOJAC, CELESTE J. BROWN, A. KEITH DUNKER, ZORAN OBRADOVIC
2005 Journal of Bioinformatics and Computational Biology  
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

Xin Deng, Jesse Eickholt, Jianlin Cheng
2012 Molecular Biosystems  
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

Heidi Ali, Siddhaling Urolagin, Ömer Gurarslan, Mauno Vihinen
2014 Human Mutation  
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

S. P. John, T. Wang, S. Steffen, S. Longhi, C. S. Schmaljohn, C. B. Jonsson
2007 Journal of Virology  
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

Predrag Radivojac, Lilia M. Iakoucheva, Christopher J. Oldfield, Zoran Obradovic, Vladimir N. Uversky, A. Keith Dunker
2007 Biophysical Journal  
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

Philippe Lieutaud, François Ferron, Alexey V. Uversky, Lukasz Kurgan, Vladimir N. Uversky, Sonia Longhi
2016 Intrinsically Disordered Proteins  
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

Xiaolin Sun, William T. Jones, Dawn Harvey, Patrick J. B. Edwards, Steven M. Pascal, Christopher Kirk, Thérèse Considine, David J. Sheerin, Jasna Rakonjac, Christopher J. Oldfield, Bin Xue, A. Keith Dunker (+1 others)
2010 Journal of Biological Chemistry  
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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