PONDR-FIT protocols

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PONDR-FIT specifications

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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 No

Publication for PONDR-FIT

PONDR-FIT in pipelines

 (4)
2015
PMCID: 4411401
PMID: 25932370
DOI: 10.1186/s40064-015-0956-0

[…] we used the build homology models module in ds to perform homology modeling of tyrosinase. we confirmed the tyrosinase-modeled structure by ramachandran plot with rampage mode in ds., we used the pondr-fit protocol in the disprot website to exclude the disordered residues of the tyrosinase 3d structure., a docking protocol was performed with tyrosinase for all small compounds from the tcm […]

2014
PMCID: 4034719
PMID: 24899913
DOI: 10.1155/2014/928589

[…] linear potentials (plp), and potential of mean force (pmf) were calculated by the ligandfit module in ds 2.5 [, ]., we drew disorder disposition to exclude disordered residues by the program of pondr-fit in the disprot website [, ]., the package of gromacs (groningen machine for chemical simulations) was used for md simulation. we employed swissparam to determine topology and parameters […]

2014
PMCID: 4090515
PMID: 25045703
DOI: 10.1155/2014/798742

[…] protein data bank (pdb id: 1urw). the resolution of its crystal structure was from residue 1 to 298, and key residues of the binding sites are located at lys33, asp86, asp127, asn132, and asp145 []. pondr-fit program in the disprot website was employed to exclude the disordered residues of 3d structure of cdk2 [, ]. this experiment utilized the ligandfit program of discovery studio (ds) 2.5 […]

2014
PMCID: 4096009
PMID: 25089269
DOI: 10.1155/2014/429486

[…] of gromacs protocols, and the presumable pathways for small molecule under dynamic conditions were analyzed by the caver 3.0 program []., the disordered disposition of traf6 protein was predicted by pondr-fit protocol [] with the sequence from swiss-prot (uniprotkb: q9y4k3). the result displayed in indicates that the key residues in the binding domain do not lie in disordered disposition […]


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PONDR-FIT in publications

 (94)
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® […]

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 […]

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., […]

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, […]

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 […]


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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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