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Protocols

H2DB specifications

Information


Unique identifier OMICS_20776
Name H2DB
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Yasukazu kamura

Additional information


http://tga.nig.ac.jp/h2db/Help

Publication for H2DB

H2DB citations

 (8)
library_books

Identification of apoB‐100 Peptide‐Specific CD8+ T Cells in Atherosclerosis

2017
PMCID: 5586274
PMID: 28711866
DOI: 10.1161/JAHA.116.005318

[…] binding predictions were made using the IEDB analysis resource Consensus tool, which combines predictions from ANN aka NetMHC (3.4),, SMM, and Comblib. Peptide length was based on optimal binding on H2Db (nanomers) or H2Kb (octamers). We therefore contracted ProImmune to assess binding of the p210 peptide to the mouse H‐2Db and H2‐Kb. ProImmune's REVEAL screening for peptide binding indicated no […]

call_split

Identification of new MUC1 epitopes using HLA transgenic animals: implication for immunomonitoring

2017
J Transl Med
PMCID: 5499006
PMID: 28679396
DOI: 10.1186/s12967-017-1254-0
call_split See protocol

[…] cubated for 30 min at room temperature with 2.5 μL of phycoerythrin (PE)-conjugated HLA-MUC1-peptide tetramer (TC Metrix, Epalinges, Switzerland) or chimeric (HLA-A2 α1 + 2, H2Kb α3 or HLA-B7 α1 + 2, H2Db α3) MUC1-peptide containing tetramer (S. Buus, Copenhagen University, Denmark). Cells were then stained with NearIR LIVE/DEAD marker (Molecular Probes, Paris, France) for 15 min. After washing, c […]

library_books

A Mouse Model of Chronic West Nile Virus Disease

2016
PLoS Pathog
PMCID: 5091767
PMID: 27806117
DOI: 10.1371/journal.ppat.1005996

[…] wing preparation of single cell suspensions, cells were plated at 1 x 106 cells/well and stained for surface markers for 15 minutes on ice. For tetramer staining, cells were stained with the WNV NS4b-H2Db tetramer (generated by the Immune Monitoring Lab, Fred Hutchinson Cancer Research Center). Cells were subsequently fixed, permeabilized (Foxp3 Fixation/Permeabilization Concentrate and Diluent, E […]

call_split

Genetic Diversity in the Collaborative Cross Model Recapitulates Human West Nile Virus Disease Outcomes

2015
MBio
PMCID: 4436067
PMID: 25944860
DOI: 10.1128/mBio.00493-15
call_split See protocol

[…] ollowing preparation of single-cell suspensions, cells were plated at 1 × 106 cells/well and stained for surface markers for 15 min on ice. For tetramer staining, cells were stained with the WNV NS4b-H2Db tetramer (generated by the Immune Monitoring Lab, Fred Hutchinson Cancer Research Center). Cells were subsequently fixed, permeabilized (Foxp3 fixation/permeabilization concentrate and diluent; e […]

call_split

Optimization of a gene electrotransfer procedure for efficient intradermal immunization with an hTERT based DNA vaccine in mice

2014
PMCID: 4362362
PMID: 26015983
DOI: 10.1038/mtm.2014.45
call_split See protocol

[…] hTERT peptides restricted to HLA-B*0702 class I molecules have been previously described., Other peptides were predicted by in-silico epitope prediction in order to bind mouse MHC class I, H2Kb, H2Db using four algorithms available online: Syfpeithi (http://www.syfpeithi.de/), Bimas (http://www-bimas.cit.nih.gov), NetMHCpan and SMM (http://tools.immuneepitope.org/main/). All synthetic peptide […]

library_books

Protective Efficacy of Cross Reactive CD8+ T Cells Recognising Mutant Viral Epitopes Depends on Peptide MHC I Structural Interactions and T Cell Activation Threshold

2010
PLoS Pathog
PMCID: 2920842
PMID: 20711359
DOI: 10.1371/journal.ppat.1001039

[…] olecule (residues 191–201; 220–228 and 247–254) have been removed from the final model due to missing electronic density. Final refinement statistics are summarized in Table I, the coordinates of the H2Db-NP-N3A complex have been deposited with the Protein Data Bank under accession numbers 3FTG. […]

Citations

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H2DB institution(s)
Genome Informatics Laboratory, Shizuoka, Japan; Plant Genetics Laboratory, National Institute of Genetics, Mishima, Japan; Citrus Research Division, NARO Institute of Fruit Tree Science, Shimizu, Japan
H2DB funding source(s)
Supported by Transdisciplinary Research Integration Center Project of Research Organization of information and Systems and Japan Society for the Promotion of Science (JSPS) KAKENHI [24500366].

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