PHDhtm statistics

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PHDhtm specifications

Information


Unique identifier OMICS_07184
Name PHDhtm
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PHDhtm

PHDhtm in publications

 (21)
PMCID: 5617230
PMID: 28915270
DOI: 10.1371/journal.pntd.0005891

[…] 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 “predict protein” web services [,]., g. […]

PMCID: 5510769
PMID: 28747815
DOI: 10.1177/1176934317713484

[…] (http://www.predictprotein.org), protscale and signalp programs (http://au.expasy.org), and signal-blast (https://www.came.sbg.ac.at/). transmembrane predictions were made using several programs: phdhtm algorithm (neural networks) using predictprotein; tmhmm server 2 (hidden markov model) at the www.cbs.dtu.dk interface; phobius (homology-supported prediction including signal peptide […]

PMCID: 5577925
PMID: 28753126
DOI: 10.7554/eLife.26067.018

[…] using a hidden markov model (; )., the hxb2 sequence of gp160’s 70 n-terminal residues was used to identify predicted tm spans with algorithms hmmtop (; ), tmpred (), tmhmm (; ), toppred (; ), phdhtm (), ∆gapp tm full protein scan with tm lengths of 12–24 residues (), and netsurfp ()., this paper was supported by the following grants:, http://dx.doi.org/10.13039/501100003246nederlandse […]

PMCID: 5172438
PMID: 15629037
DOI: 10.1016/S1672-0229(04)02001-7

[…] mps extracted from swiss-prot that have experimentally defined topologies., the five widely used prediction methods for predicting the topology of α-helix bundle mps are tmhmm , hmmtop , memsat , phdhtm , and toppred . tmhmm, hmmtop, and memsat are all based on hmms with 5~7 types of structural states. phdhtm is designed to use information from homologous proteins. toppred was the first […]

PMCID: 4921136
PMID: 27382485
DOI: 10.1155/2016/1968493

[…] and consurf (http://consurf.tau.ac.il/) was used to calculate the evolutionary conservation score for all ubiad1 residues [, ]. seven different modeling algorithms (tmpred, phdhtm, tmhmm 2.0, hmmtop 2.0, memsat3, memsat-svm, and tmseg) were used to predict the transmembrane helices of both wild type and mutant forms of ubiad1 [–]. topo2 (http://www.sacs.ucsf.edu/topo2/) […]


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PHDhtm institution(s)
European Molecular Biology Laboratory, Heidelberg, Germany

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