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Protocols

PROFbval specifications

Information


Unique identifier OMICS_09791
Name PROFbval
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for PROFbval

PROFbval citations

 (14)
library_books

Elongation factor Tu is a multifunctional and processed moonlighting protein

2017
Sci Rep
PMCID: 5593925
PMID: 28894125
DOI: 10.1038/s41598-017-10644-z

[…] acid interaction sites were identified using ISIS. Intrinsically disordered regions were predicted by Meta-Disorder, , which combines the outputs from original prediction methods NORSnet, DISOPRED2, PROFbval and Ucon. Solvent accessibility of each amino acid position was ascertained using evolutionary information from multiple sequence alignments and a multi-level system. Nucleotide, DNA and RNA […]

library_books

Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment Based Protein Structure Predictions

2017
Sci Rep
PMCID: 5539115
PMID: 28765603
DOI: 10.1038/s41598-017-07156-1

[…] he average, especially in the presence of outliers. Overall, FRAGFOLD-IDP and DynaMine clearly perform best and significantly better than the naïve method (Wilcoxon signed-rank test p-value = 0.004). PROFbval predictions and IUpred achieve performance on par with the naïve approach. DISOPRED3 achieves higher median RS than the naïve, but the result is not statistically significant (p-value = 0.73) […]

library_books

Predicting MoRFs in protein sequences using HMM profiles

2016
BMC Bioinformatics
PMCID: 5259822
PMID: 28155710
DOI: 10.1186/s12859-016-1375-0

[…] sidues within the protein sequence, position specific scoring matrices (PSSM) extracted using PSI-BLAST [], relative solvent accessibility given by Real-SPINE3 [], flexibility (B-factor) estimated by PROFbval [], and the predictions of five different intrinsic disorder predictors are used. Finally, using PSI-BLAST [], MoRFpred aligns the query sequence to the training sequences and calculates an e […]

library_books

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

2016
BMC Genomics
PMCID: 4765031
PMID: 26911138
DOI: 10.1186/s12864-016-2456-1

[…] omology to known proteins, []), SEG (low- and high-complexity regions, []), ConSurf (evolutionary conservation of amino acids, []), DISULFIND (disulfide bonds, []). For disordered region predictions, PROFbval [], UCON [] and METADISORDER [] were used. Further, PROFtmb (bacterial transmembrane β-barrels, []), Metastudent (Gene Ontology terms, []), and LocTree3 (subcellular localization, []) were ap […]

call_split

A mutation in the POT1 gene is responsible for cardiac angiosarcoma in TP53 negative Li–Fraumeni like families

2015
Nat Commun
PMCID: 4598567
PMID: 26403419
DOI: 10.1038/ncomms9383
call_split See protocol

[…] minimum REPROFSEc score of 5) of conserved secondary structures and evolutionary profiles for POT1 carrying the p.R117C mutation were based on several original prediction methods (NORSnet, DISOPRED2, PROFbval and Ucon) implemented in PredictProtein. Solvent accessibility notation (PACC) was annotated using the PROFAcc prediction algorithm also implemented in ProteinPredict. Protein binding regions […]

library_books

Protein flexibility in the light of structural alphabets

2015
Front Mol Biosci
PMCID: 4445325
PMID: 26075209
DOI: 10.3389/fmolb.2015.00020

[…] Based on the previously defined flexibility classes of these structural candidates, the prediction of target flexibility is made. Interestingly, the prediction rate is slightly better than the one of PROFbval (Schlessinger et al., ) that was optimized for only two classes.Hence, the originality of the method lies (i) in the use of a combination of B-factors and RMSF for quantifying protein dynamic […]

Citations

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PROFbval institution(s)
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA

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