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PONDR-FIT specifications

Information


Unique identifier OMICS_03617
Name PONDR-FIT
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability No
Maintained Yes

Publication for PONDR-FIT

PONDR-FIT citations

 (94)
library_books

Deciphering the dark proteome of Chikungunya virus

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

[…] more accurate evaluations of disordered regions in a query protein, whereas pondr® vlxt is known as the most sensitive 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® […]

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

[…] and the results obtained were compared to each other., shows the number of disordered amino acids at the two termini and the overall percentage of intrinsic disorder of e6 proteins, analyzed by the pondr-fit software []., the n-terminal and c-terminal ends of the high-risk hpv e6 proteins were observed to have a higher number of disordered amino acids and a higher percentage of id relative […]

library_books

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual family Immunophilin Chaperones

2017
Comput Struct Biotechnol J
PMCID: 5852385
PMID: 29552333
DOI: 10.1016/j.csbj.2017.12.002

[…] and the prdos results agreed with essentially all of them, including several meta-predictors (data not shown), such as metadisorder, which compares nearly two dozen different methods [], and pondr-fit, which combines five []. for routine analysis, the prdos results were downloaded as csv (comma-separated values) files, and then imported into excel for further analysis and graphing., […]

library_books

Phosphorylation of multiple sites within an acidic region of Alcadein α is required for kinesin 1 association and Golgi exit of Alcadein α cargo

2017
Mol Biol Cell
PMCID: 5739299
PMID: 29093024
DOI: 10.1091/mbc.E17-05-0301

[…] the golgi exit of alcα and app remains unclear. furthermore, an acidic region, which resides between wd1 and wd2 in the alcα cytoplasmic region, was predicted to be intrinsically disordered by the pondr-fit prediction tool (), but the role of this large acidic region in the function and/or metabolism of alcα has not been revealed., together with alcα, other membrane proteins including app, […]

library_books

Disulfide driven folding for a conditionally disordered protein

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

[…] 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 (fig. )., previous folding […]

library_books

Characterization of Soft Amyloid Cores in Human Prion Like Proteins

2017
Sci Rep
PMCID: 5608858
PMID: 28935930
DOI: 10.1038/s41598-017-09714-z

[…] to protein sequences., an analysis of the structural context in which these soft amyloid cores are embedded in their respective sequences using the prediction algorithms foldindex, iupred, pondr-fit and ronn indicates that they are preferentially located in disordered protein segments (table )., we synthetized 21-residues long peptides correspondent to the detected amyloid cores […]


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PONDR-FIT institution(s)
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA

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