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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 citations

 (13)
library_books

Discovery of Novel Leptospirosis Vaccine Candidates Using Reverse and Structural Vaccinology

2017
Front Immunol
PMCID: 5406399
PMID: 28496441
DOI: 10.3389/fimmu.2017.00463

[…] us, 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, 108 […]

call_split

Consensus computational network analysis for identifying candidate outer membrane proteins from Borrelia spirochetes

2016
BMC Microbiol
PMCID: 4939628
PMID: 27400788
DOI: 10.1186/s12866-016-0762-z
call_split See protocol

[…] the Phobius server [] and the TMHMM server []. Outer membrane (OM) localization was next predicted by CELLO [] and PSORTb 3.0 []. The following servers were utilized to predict β-barrel conformation: HHOMP [], TMBETADISC-AAC [], PRED-TMBB [, ], and BOMP []. After all sequences were examined by the above algorithms, a candidate OMP list was generated according to the following steps: (1) any protei […]

library_books

Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore Forming Proteins

2016
PLoS One
PMCID: 4827864
PMID: 27064789
DOI: 10.1371/journal.pone.0152733

[…] parent 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 co […]

library_books

Contact and Protein Transfer Dependent Stimulation of Assembly of the Gliding Motility Machinery in Myxococcus xanthus

2015
PLoS Genet
PMCID: 4488436
PMID: 26132848
DOI: 10.1371/journal.pgen.1005341

[…] nal 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, […]

call_split

Prediction of structural features and application to outer membrane protein identification

2015
Sci Rep
PMCID: 4478468
PMID: 26104144
DOI: 10.1038/srep11586
call_split See protocol

[…] We used the same library and test dataset (i.e., R-dataset) as HHomp to assess our OMP identification method. The performance of OMP identification was compared via ROC analysis. We paid more attention to the performance at <1% (e.g., 50 false positive instances […]

call_split

Quantitative proteomic analysis of host—pathogen interactions: a study of Acinetobacter baumannii responses to host airways

2015
BMC Genomics
PMCID: 4449591
PMID: 26025090
DOI: 10.1186/s12864-015-1608-z
call_split See protocol

[…] Protein function was determined by http://www.ncbi.nlm.nih.gov.HHomp, http://toolkit.tuebingen.mpg.de/hhomp# was used for the prediction of outer membrane proteins.The presence of export signals was predicted by use of a combination of algorithms (SignalP 4.1 (ht […]

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

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