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HistoneDB specifications


Unique identifier OMICS_11350
Name HistoneDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 2.0
Maintained Yes


  • person_outline An Panchenko

Additional information


Publications for HistoneDB

HistoneDB citations


Systematic quantitative analysis of H2A and H2B variants by targeted proteomics

PMCID: 5767011
PMID: 29329550
DOI: 10.1186/s13072-017-0172-y

[…] Mass spectrometry RAW files were submitted to Mascot Daemon (version 2.5.1). MS/MS data acquired on histones were matched to the mouse MS_HistoneDB [] and to a list of about 500 contaminants including keratins, trypsin, etc. The following modifications were considered as variable ones: N-terminal protein acetylation; Lys acetylation; Ly […]


Hydroxyl radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning

Nucleic Acids Res
PMCID: 5765820
PMID: 28934480
DOI: 10.1093/nar/gkx616

[…] c nucleosome with 601TA DNA sequence (601TA-NUC) was built based on Xenopus laevis nucleosome structure with 601 DNA (PDB ID: 3LZ0) using Modeller () and 3DNA (). Histone sequences were obtained from HistoneDB 2.0 database (). The model of yeast centromeric nucleosome on CEN3 DNA sequence (CEN3-NUC) was built using the same methods based on X. laevis nucleosome structure with α-satellite DNA (PDB […]


MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

PMCID: 5223428
PMID: 28096900
DOI: 10.1186/s13072-016-0109-x

[…] ]*\) and the description rule \(.*\). In addition, the taxonomy and sequence report sources are indicated as “Swiss-Prot FASTA” and “FASTA file”, respectively. No taxonomy was specified when using MS_HistoneDB with Mascot Daemon.Classical histone modifications were included in the variable modifications: N-terminal protein acetylation; Lys acetylation; and Lys and Arg mono- or di-methylation. For […]


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HistoneDB institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
HistoneDB funding source(s)
Supported by the Intramural Research Program of the National Library of Medicine, NIH and by the US-Russia Collaboration in the Biomedical Sciences NIH visiting fellows program.

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