Histone Database

Histone Database
Content
Description	curated database of histone proteins and their variants
Contact
Research center	National Center for Biotechnology Information
Primary citation	Draizen EJ, Shaytan AK, Marino-Ramirez L, Talbert PB, Landsman D, Panchenko AR (2016)[1]
Access
Website	https://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0

The Histone Database is a comprehensive database of histone protein sequences including histone variants, classified by histone types and variants, maintained by National Center for Biotechnology Information. The creation of the Histone Database was stimulated by the X-ray analysis of the structure of the nucleosomal core histone octamer[2] followed by the application of a novel motif searching method to a group of proteins containing the histone fold motif in the early-mid-1990.[3] The first version of the Histone Database was released in 1995[4] and several updates have been released since then.[5][6][7][8][9][10][11]

Current version of the Histone Database - HistoneDB 2.0 - with variants - includes sequence and structural annotations for all five histone types (H3, H4, H2A, H2B, H1) and major histone variants within each histone type. It has many interactive tools to explore and compare sequences of different histone variants from various organisms. The core of the database is a manually curated set of histone sequences grouped into 30 different variant subsets with variant-specific annotations. The curated set is supplemented by an automatically extracted set of histone sequences from the non-redundant protein database using algorithms trained on the curated set. The interactive web site supports various searching strategies in both datasets: browsing of phylogenetic trees; on-demand generation of multiple sequence alignments with feature annotations; classification of histone-like sequences and browsing of the taxonomic diversity for every histone variant.

References

Draizen EJ, Shaytan AK, Marino-Ramirez L, Talbert PB, Landsman D, Panchenko AR (2016). "HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants". Database: The Journal of Biological Databases and Curation. 2016: baw014. doi:10.1093/database/baw014. PMC 4795928. PMID 26989147.
Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN (1991). "The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix". Proc Natl Acad Sci U S A. 88 (22): 10148–52. Bibcode:1991PNAS...8810148A. doi:10.1073/pnas.88.22.10148. PMC 52885. PMID 1946434.
Baxevanis AD, Arents G, Moudrianakis EN, Landsman D (1995). "A variety of DNA-binding and multimeric proteins contain the histone fold motif". Nucleic Acids Res. 23 (14): 2685–91. doi:10.1093/nar/23.14.2685. PMC 307093. PMID 7651829.
Baxevanis AD, Landsman D (1996). "Histone Sequence Database: a compilation of highly-conserved nucleoprotein sequences". Nucleic Acids Res. 24 (1): 245–7. doi:10.1093/nar/24.1.245. PMC 145601. PMID 8594591.
Marino-Ramirez L, Levine KM, Morales M, Zhang S, Moreland RT, Baxevanis AD, Landsman D (2011). "The Histone Database: an integrated resource for histones and histone fold-containing proteins". Database: The Journal of Biological Databases and Curation. 2011: bar048. doi:10.1093/database/bar048. PMC 3199919. PMID 22025671.
Marino-Ramirez L, Hsu B, Baxevanis AD, Landsman D (2006). "The Histone Database: a comprehensive resource for histones and histone fold-containing proteins". Proteins. 62 (4): 838–42. doi:10.1002/prot.20814. PMC 1800941. PMID 16345076.
Sullivan S, Sink DW, Trout KL, Makalowska I, Taylor PM, Baxevanis AD, Landsman D (2002). "The Histone Database". Nucleic Acids Res. 30 (1): 341–2. doi:10.1093/nar/30.1.341. PMC 99096. PMID 11752331.
Sullivan SA, Aravind L, Makalowska I, Baxevanis AD, Landsman D (2000). "The histone database: a comprehensive WWW resource for histones and histone fold-containing proteins". Nucleic Acids Res. 28 (1): 320–2. doi:10.1093/nar/28.1.320. PMC 102427. PMID 10592260.
Makalowska I, Ferlanti ES, Baxevanis AD, Landsman D (1999). "Histone Sequence Database: sequences, structures, post-translational modifications and genetic loci". Nucleic Acids Res. 27 (1): 323–4. doi:10.1093/nar/27.1.323. PMC 148172. PMID 9847217.
Baxevanis AD, Landsman D (1998). "Histone Sequence Database: new histone fold family members". Nucleic Acids Res. 26 (1): 372–5. doi:10.1093/nar/26.1.372. PMC 147196. PMID 9399877.
Baxevanis AD, Landsman D (1997). "Histone and histone fold sequences and structures: a database". Nucleic Acids Res. 25 (1): 272–3. doi:10.1093/nar/25.1.272. PMC 146383. PMID 9016552.

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[HistDBpaper-1] Draizen EJ, Shaytan AK, Marino-Ramirez L, Talbert PB, Landsman D, Panchenko AR (2016). "HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants". Database: The Journal of Biological Databases and Curation. 2016: baw014. doi:10.1093/database/baw014. PMC 4795928. PMID 26989147.

[HistPaper1-2] Arents G, Burlingame RW, Wang BC, Love WE, Moudrianakis EN (1991). "The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix". Proc Natl Acad Sci U S A. 88 (22): 10148–52. Bibcode:1991PNAS...8810148A. doi:10.1073/pnas.88.22.10148. PMC 52885. PMID 1946434.

[HistPaper2-3] Baxevanis AD, Arents G, Moudrianakis EN, Landsman D (1995). "A variety of DNA-binding and multimeric proteins contain the histone fold motif". Nucleic Acids Res. 23 (14): 2685–91. doi:10.1093/nar/23.14.2685. PMC 307093. PMID 7651829.

[HistDBpaper8-4] Baxevanis AD, Landsman D (1996). "Histone Sequence Database: a compilation of highly-conserved nucleoprotein sequences". Nucleic Acids Res. 24 (1): 245–7. doi:10.1093/nar/24.1.245. PMC 145601. PMID 8594591.

[HistDBpaper1-5] Marino-Ramirez L, Levine KM, Morales M, Zhang S, Moreland RT, Baxevanis AD, Landsman D (2011). "The Histone Database: an integrated resource for histones and histone fold-containing proteins". Database: The Journal of Biological Databases and Curation. 2011: bar048. doi:10.1093/database/bar048. PMC 3199919. PMID 22025671.

[HistDBpaper2-6] Marino-Ramirez L, Hsu B, Baxevanis AD, Landsman D (2006). "The Histone Database: a comprehensive resource for histones and histone fold-containing proteins". Proteins. 62 (4): 838–42. doi:10.1002/prot.20814. PMC 1800941. PMID 16345076.

[HistDBpaper3-7] Sullivan S, Sink DW, Trout KL, Makalowska I, Taylor PM, Baxevanis AD, Landsman D (2002). "The Histone Database". Nucleic Acids Res. 30 (1): 341–2. doi:10.1093/nar/30.1.341. PMC 99096. PMID 11752331.

[HistDBpaper4-8] Sullivan SA, Aravind L, Makalowska I, Baxevanis AD, Landsman D (2000). "The histone database: a comprehensive WWW resource for histones and histone fold-containing proteins". Nucleic Acids Res. 28 (1): 320–2. doi:10.1093/nar/28.1.320. PMC 102427. PMID 10592260.

[HistDBpaper5-9] Makalowska I, Ferlanti ES, Baxevanis AD, Landsman D (1999). "Histone Sequence Database: sequences, structures, post-translational modifications and genetic loci". Nucleic Acids Res. 27 (1): 323–4. doi:10.1093/nar/27.1.323. PMC 148172. PMID 9847217.

[HistDBpaper6-10] Baxevanis AD, Landsman D (1998). "Histone Sequence Database: new histone fold family members". Nucleic Acids Res. 26 (1): 372–5. doi:10.1093/nar/26.1.372. PMC 147196. PMID 9399877.

[HistDBpaper7-11] Baxevanis AD, Landsman D (1997). "Histone and histone fold sequences and structures: a database". Nucleic Acids Res. 25 (1): 272–3. doi:10.1093/nar/25.1.272. PMC 146383. PMID 9016552.