PROFtmb protocols

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PROFtmb specifications

Information


Unique identifier OMICS_16019
Name PROFtmb
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A protein sequence (raw).
Input format FASTA-like (text)
Output data A protein report.
Output format A sequence feature annotation format.
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0
Stability Stable
Source code URL https://rostlab.org/owiki/index.php/Packages
Maintained Yes

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Maintainer


  • person_outline Henry Bigelow <>

Publications for PROFtmb

PROFtmb in pipeline

2017
PMCID: 5662880
PMID: 29123525
DOI: 10.3389/fimmu.2017.01382

[…] in brief, the tool uses hidden markov model to predict transmembrane state of the input sequences and the krogh et al. reported 97–98% prediction sensitivity ()., the tmb was computed using proftmb tool, which is also a hidden markov model-based prediction program (). only tmb of g− pathogen sequences were computed because classical g+ bacteria do not contain β-barrel membrane proteins […]


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PROFtmb in publications

 (13)
PMCID: 5662880
PMID: 29123525
DOI: 10.3389/fimmu.2017.01382

[…] in brief, the tool uses hidden markov model to predict transmembrane state of the input sequences and the krogh et al. reported 97–98% prediction sensitivity ()., the tmb was computed using proftmb tool, which is also a hidden markov model-based prediction program (). only tmb of g− pathogen sequences were computed because classical g+ bacteria do not contain β-barrel membrane proteins […]

PMCID: 4705124
PMID: 26400107
DOI: 10.1007/s00203-015-1154-8

[…] et al. ). alignments were edited by visual inspection and modified in microsoft word. wspb protein structure predictions were obtained using tools available at www.predictprotein.org, including the proftmb program (dell et al. ) for prediction of bacterial transmembrane beta barrels (bigelow et al. ) and per-residue prediction of up-strand, down-strand, periplasmic loop and outer loop positions […]

PMCID: 4274882
PMID: 25566294
DOI: 10.3389/fpls.2014.00722

[…] (walther et al., ). however, the m-domains of bstoc159 and a. thaliana homologs have a negligible probability (p = 0.05) of adopting a transmembrane β-barrel conformation, according to the proftmb prediction program (http://www.predictprotein.org; bigelow et al., ). on the other hand, a blast search of the structural database deposited in the protein data bank (pdb) using the a. […]

PMCID: 3732596
PMID: 23971032
DOI: 10.1155/2013/398968

[…] sites—“profisis” []; disulfide bridges—“disulfinder” []; nonregular secondary structure—“norsp” []; pfam hits—“hmmer” [, ]; local complexity—“ncbi-seg” []; bacterial transmembrane beta barrels—“proftmb” []; coiled-coils—“ncoils” []; protein residue flexibility—“profbval” []; sequence homologies—“blast2” []; protein feature prediction suite—“predictprotein” []., these tools are available […]

PMCID: 3582582
PMID: 23013516
DOI: 10.1186/1471-2164-13-510

[…] [-]. we used hhomp [] to classify the proteins into different omp families. a brief summary of the omp classification obtained from hhomp [] for our data set is shown in table . we then used proftmb [] and psipred [] annotations to identify and extract the c-terminal β-strands from the omps. to evaluate the phenomenon of species specificity, we initially tried to cluster the c-terminal […]


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PROFtmb funding source(s)
This work was supported by grant R01-LM07329-01 from the National Library of Medicine.

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