FoldIndex statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FoldIndex
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Tool usage distribution map

This map represents all the scientific publications referring to FoldIndex per scientific context
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Protocols

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 citations

 (133)
library_books

Deciphering the dark proteome of Chikungunya virus

2018
Sci Rep
PMCID: 5895634
PMID: 29643398
DOI: 10.1038/s41598-018-23969-0

[…] sitive 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 in […]

call_split

Comparative genomic analysis of mollicutes with and without a chaperonin system

2018
PLoS One
PMCID: 5810989
PMID: 29438383
DOI: 10.1371/journal.pone.0192619
call_split See protocol

[…] 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 again for the g […]

library_books

SUMO targeting of a stress tolerant Ulp1 SUMO protease

2018
PLoS One
PMCID: 5774762
PMID: 29351565
DOI: 10.1371/journal.pone.0191391

[…] ive 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 the ). […]

library_books

Understanding the Role of Intrinsic Disorder of Viral Proteins in the Oncogenicity of Different Types of HPV

2018
Int J Mol Sci
PMCID: 5796147
PMID: 29315236
DOI: 10.3390/ijms19010198

[…] dict 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 or disorder […]

library_books

Disulfide driven folding for a conditionally disordered protein

2017
Sci Rep
PMCID: 5717278
PMID: 29208936
DOI: 10.1038/s41598-017-17259-4

[…] Intrinsic disorder in hCox17 was predicted using the web-based algorithms FoldIndex, IUPRED, ESpritz, PONDR-FIT and RONN with default settings. An 11-residue sliding window was used in all cases. […]

library_books

Structural disorder and induced folding within two cereal, ABA stress and ripening (ASR) proteins

2017
Sci Rep
PMCID: 5686140
PMID: 29138428
DOI: 10.1038/s41598-017-15299-4

[…] ), both proteins appear depleted in hydrophobic clusters, indicative of protein disorder (Fig. ). Additionally, the two proteins are predicted to be disordered over most of their sequence by DorA and FoldIndex (Supplementary Text ). In further support of this, both proteins are predicted to be disordered over their entire sequence by MetaDisorderMD2 (Fig. ), the most accurate disorder predictor ac […]


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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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