HHomp specifications

Information


Unique identifier OMICS_07179
Name HHomp
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for HHomp

HHomp in publications

 (13)
PMCID: 5406399
PMID: 28496441
DOI: 10.3389/fimmu.2017.00463

[…] tmhmm, hhtop, and memsat) determined that 3,302 proteins did not contain a tmh, this was reduced to 2,929 proteins by all 4 predictors. the transmembrane β-barrel (βb) structure predictors (bomp, hhomp, tmbetadisc-rbf, and mcmbb) identified 1,085 βb-omps, 20 of which were confirmed by all 4 predictors. finally, 230 proteins were identified as lipoproteins by at least one of the predictors, […]

PMCID: 4939628
PMID: 27400788
DOI: 10.1186/s12866-016-0762-z

[…] [] and/or psortb 3.0 []] was retained as a candidate omp and was then examined for β-barrel topology given that all structurally characterized omps from diderm organisms form β-barrels. the programs hhomp [], tmbdisc-acc [], pred-tmbb [], and bomp [] were used to examine β-barrel propensity, and proteins were retained if they were predicted to be a β-barrel by at least one of the four or two […]

PMCID: 4827864
PMID: 27064789
DOI: 10.1371/journal.pone.0152733

[…] that many of the families in tcdb often correlate with those in pfam and ompdb, and some of the tc families found within a single superfamily are also found in single clans in pfam., while pfam, hhomp and ompdb are based substantially on hmms as noted above, tcdb is based largely on the superfamily principle, also known as the transitivity rule. surprisingly, perhaps, there is considerable […]

PMCID: 4488436
PMID: 26132848
DOI: 10.1371/journal.pgen.1005341

[…] peptides were identified using the signalp [] and lipop [] webservers, respectively. trans-membrane α-helices were identified using the das webserver []. om β-barrel domains were identified using hhomp []. the hmmer3 software package [] was used in conjunction with the pfam26 domain library [] for domain architecture analysis with default gathering thresholds. in the event of domain overlaps, […]

PMCID: 4478468
PMID: 26104144
DOI: 10.1038/srep11586

[…] for proteome annotation and drug design. during the past decades, omp identification techniques have received considerable attention and a series of novel methods (e.g., tmbeta-net, pred-tmbb, and hhomp) has been developed. machine learning methods were also used in omp identification. one successful tool is hhomp. to predict whether a query sequence is an omp, hhomp builds a profile hmm […]


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HHomp institution(s)
Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, Tübingen, Germany

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