FoldIndex protocols

View FoldIndex computational protocol

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FoldIndex specifications

Information


Unique identifier OMICS_03624
Name FoldIndex
Interface Web user interface
Restrictions to use None
Input data Protein sequence
Output data Protein disorder plot or text
Output format TXT
Programming languages Javascript, Python
Database management system MySQL
Computer skills Basic
Stability Stable
Maintained Yes

Publication for FoldIndex

FoldIndex in pipelines

 (2)
2015
PMCID: 4499774
PMID: 25826651
DOI: 10.3390/life5021141

[…] using jpred3 (http://www.compbio.dundee.ac.uk/www-jpred/) []. folding potential was evaluated by the feed-forward neural networks based prediction algorithm, pondr (http://pondr.com) [,] as well as foldindex (http://bip.weizmann.ac.il/fldbin/findex) []. ab initio protein structure prediction for each m-repeat with flanking sequences was performed at the quark server […]

2012
PMCID: 3274520
PMID: 22347381
DOI: 10.1371/journal.pone.0030534

[…] 266–318), predicted by psipred., the prediction of disorder in the mnv-1 ns1-2 protein also occurs for the ns1-2 protein of other norovirus genogroups, including human noroviruses, as shown by the foldindex predictions in , confirming that this disordered region is not unique to murine norovirus. significant sequence divergence between related proteins is commonly observed in regions […]


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FoldIndex in publications

 (118)
PMCID: 5895634
PMID: 29643398
DOI: 10.1038/s41598-018-23969-0

[…] predictor for finding disordered based interaction sites, and a meta-predictor pondr-fit as is more accurate than its individual component predictors, such as pondr® vls2, pondr® vlxt, iupred, foldindex, topidp. in our study, we have used pondr® fit, pondr® vsl2, and pondr® vlxt for disordered analysis in polyprotein of chikv. several reports suggested that idps/idprs play a central role […]

PMCID: 5810989
PMID: 29438383
DOI: 10.1371/journal.pone.0192619

[…] mollicute species were downloaded since for 3 genomes the cds are not available. the silva database [] was used to retrieve 16s rrna sequences (ssu) of the mollicute species., for length, charge and foldindex comparisons, the mean of all homologs found in groe+ or groe- of one query protein was calculated and then all (57 or less) the means (per groe+ or groe- group) were averaged […]

PMCID: 5774762
PMID: 29351565
DOI: 10.1371/journal.pone.0191391

[…] bioinformatics analysis of k. marxianus and s. pombe proteins []. we observed the biggest size difference between kmulp1 and sculp1 (66 amino acids) and km and sc siz1 (99 amino acids). using the foldindex webs-tool, we generated the predicted unfoldability scores for all sumo pathway components []. we found that, as expected, km sumo pathway components were general less disordered (see […]

PMCID: 5796147
PMID: 29315236
DOI: 10.3390/ijms19010198

[…] regions of intrinsic disorder in e6 proteins of different hpv types., pondr-fit employs the unification of the methodologies of six predictors namely, pondr® vlxt, pondr® vl3, pondr® vsl2, iupred, foldindex, and topidp. the output data are composed of a table that individually scores each of the amino acids in the sequence, indicating the probability of each residue being structured […]

PMCID: 5717278
PMID: 29208936
DOI: 10.1038/s41598-017-17259-4

[…] change to simulate disulfide bond reduction. we virtually mutated cys to ser in hcox17 sequence to mimic the reduced state of the protein and analyzed the degree of predicted disorder using foldindex, espritz, iupred, pondr-fit and ronn algorithms. with the exception of a small stretch at the hcox17 c-terminus, all these programs consistently predict this sequence as mostly disordered […]


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FoldIndex institution(s)
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland; Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Poznan, Poland
FoldIndex funding source(s)
This tool was funded by Polish Ministry of Science and Higher Education (grant NN301 190139 and POIG.02.03.00-00-003/09) and the European Union (project HealthProt, contract number 229676).

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