PolyPhobius protocols

View PolyPhobius computational protocol

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PolyPhobius specifications

Information


Unique identifier OMICS_07185
Name PolyPhobius
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Erik Sonnhammer <>

Publication for PolyPhobius

PolyPhobius in pipelines

 (2)
2012
PMCID: 3430611
PMID: 22952860
DOI: 10.1371/journal.pone.0044030

[…] protein assay kit (thermo scientific, usa) according to manufacturer`s instructions., proteins were aligned using clustalw2 . positions of trans-membrane α-helices were predicted using phobius and polyphobius , . protein secondary structure was predicted using jpred 3 ., we thank i.v. meshcheryakova and j. carrere for help with cloning and genetic engineering of salmonella strains. we thank […]

2010
PMCID: 2919393
PMID: 20706583
DOI: 10.1371/journal.pntd.0000796

[…] using blast. multiple sequence alignments were performed with clustalw2 using default parameters of ktup and gap opening and gap extension penalties. transmembrane helices were predicted using polyphobius . interproscan was used to identify functional domains within the sequence. predicted n-glycosylation sites were identified using the netnglyc 1.0 server […]


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PolyPhobius in publications

 (30)
PMCID: 5823858
PMID: 29472565
DOI: 10.1038/s41598-018-21631-3

[…] were performed using mainly standard settings. high conservation filter threshold was set to 95. constraint rank weight function was set to n/i. transmembrane topology was calculated using polyphobius and validated against tmhmm2,. psipred was used to calculate predicted secondary structure. helices with a reliability index below 3 were set to strand. predictions were evaluated […]

PMCID: 5868721
PMID: 29281821
DOI: 10.1016/j.celrep.2017.12.006

[…] f (promega). reactions were incubated for 4 hr at 37°c and then tca precipitated, resuspended in laemmli sample buffer, and analyzed by sds-page., transmembrane domain predictions were made with polyphobius () and topcons (); coiled coil predictions were made with coils (). raptorx-contact () was used to calculate contact maps from alignments of 584 tmco1 (188 residues), 453 emc3 (261 […]

PMCID: 5678787
PMID: 29077760
DOI: 10.1371/journal.ppat.1006705

[…] to find domains with homologs of known structure and quick2d to identify structured and non-structured regions and putative transmembrane helices [,]. transmembrane helices were further sought with polyphobius. for putative membrane-peripheral and transmembrane helices, ideal alpha-helices were generated with the “fab” function of pymol, as were intervening loops. the ns1-2 central domain […]

PMCID: 5617230
PMID: 28915270
DOI: 10.1371/journal.pntd.0005891

[…] using a self-written python script. transmembrane helices were predicted using the programs topcons 2.0 [] (metasearch with five programs), psipred [] (memsat-svm and memsat3 algorithms), phobius/polyphobius [], tmhmm 2.0 [], tmseg, phdhtm [], tmpred [] and toppred [], and a consensus was deduced from all predictions. secondary structure predictions were done using itasser, psspred […]

PMCID: 5520436
PMID: 28559405
DOI: 10.1128/IAI.00139-17

[…] we named this gene pimms2, for midgut invasion ookinete protein screen candidate 2. bioinformatics analysis of the deduced protein sequence, using the open-access tools phyre2 (), phobius, and polyphobius (), predicted with high probability two hydrophobic regions of alpha-helix structure encompassing the amino acid residues 6 to 25 and 416 to 427, respectively (). additionally, targetp () […]


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PolyPhobius institution(s)
Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden

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