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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 citations

 (33)
library_books

Endogenous insensitivity to the Orco agonist VUAA1 reveals novel olfactory receptor complex properties in the specialist fly Mayetiola destructor

2018
Sci Rep
PMCID: 5823858
PMID: 29472565
DOI: 10.1038/s41598-018-21631-3

[…] lculations 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 against […]

library_books

Identification of Oxa1 Homologs Operating in the Eukaryotic Endoplasmic Reticulum

2017
Cell Rep
PMCID: 5868721
PMID: 29281821
DOI: 10.1016/j.celrep.2017.12.006

[…] 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 residue […]

library_books

Membrane alterations induced by nonstructural proteins of human norovirus

2017
PLoS Pathog
PMCID: 5678787
PMID: 29077760
DOI: 10.1371/journal.ppat.1006705

[…] d 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 (resid […]

call_split

The single cyclic nucleotide specific phosphodiesterase of the intestinal parasite Giardia lamblia represents a potential drug target

2017
PLoS Negl Trop Dis
PMCID: 5617230
PMID: 28915270
DOI: 10.1371/journal.pntd.0005891
call_split See protocol

[…] ted 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 and the “Pr […]

call_split

Computational genome wide survey of odorant receptors from two solitary bees Dufourea novaeangliae (Hymenoptera: Halictidae) and Habropoda laboriosa (Hymenoptera: Apidae)

2017
Sci Rep
PMCID: 5589748
PMID: 28883425
DOI: 10.1038/s41598-017-11098-z
call_split See protocol

[…] olitary bees as well as from A. mellifera - AmOrs, A. florea - AfOrs, H. saltator - HsOrs and N. vitripennis - NvOrs were subjected to transmembrane helix (TMH) prediction using HMMTOP, , TMHMM, and PolyPhobius, . Consensus TMH prediction was derived for each amino acid of all sequences based on support of at least two out of three methods and was compared across these datasets. Similarly sequenc […]

library_books

Plasmodium berghei PIMMS2 Promotes Ookinete Invasion of the Anopheles gambiae Mosquito Midgut

2017
Infect Immun
PMCID: 5520436
PMID: 28559405
DOI: 10.1128/IAI.00139-17

[…] otein. 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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