Polbase

Polbase (DNA Polymerase Database) is an open repository of DNA polymerase information.[1] Polbase captures information from published research on polymerase activity, and presents it in context with related work. Polbase indexes over 5,000 references [2] from the 1950s to the present and includes hundreds of polymerases and their related mutants. Polbase's collaborative model allows polymerase investigators to complete, correct and validate Polbase's representation of their work.

Polbase
Content
DescriptionComprehensive database covering various aspects of DNA polymerases
Data types
captured		Biology, biochemistry and structure of DNA polymerases
OrganismsPolbase organisms list
Contact
Research centerNew England Biolabs
AuthorsBrad Langhorst and Nicole Nichols
Primary citationPMID 21993301
Access
WebsitePolbase

Content

Polbase features a listing of known polymerases categorized by organism, polymerase family, and selected properties. Each indexed polymerase has its own snapshot page containing links to all its information in the database. All results in Polbase are stored with the relevant experimental details to put them into context. If structure information is available, Polbase links to the polymerase's Protein Data Bank (PDB) entry. All information gathered in Polbase is linked to the original publication where it was reported.

Features
  • Polymerases by family, organism and properties[3]
  • Search by author, organism, polymerase name, property, etc.[4]
  • Browsing by reference[5]
  • Browsing by author[6]
  • Browsing by organism[7]

Information sources

Polbase draws information from a variety of sources including PubMed, PDB, and directly from polymerase investigators.

Interconnections

Polbase is connected with various other databases. These include:

History

Polbase began in March 2009 with a grant from the NIH's SBIR program[8] and was first presented to the public at MIT's DNA and Mutagenesis Meeting [9] In March 2010 Polbase was presented to a larger audience at the Evolving Polymerases 2010 Conference.[10] Polbase was also presented in more technical detail at the Rocky 2010 ISMB Conference.[11][12] Polbase is described in more detail in the 2012 Nucleic Acids Research Database Issue.

Polbase was built at New England Biolabs by Brad Langhorst and Nicole Nichols with the help of founding collaborators Linda Reha-Krantz, Bill Jack, Cathy Joyce, Stu Linn, Stefan Sarafianos, Sam Wilson, and Roger Woodgate.

References
  1. Langhorst, Bradley W.; Jack, William E.; Reha-Krantz, Linda; Nichols, Nicole M. (2011). "Polbase: A repository of biochemical, genetic and structural information about DNA polymerases". Nucleic Acids Research. 40 (Database issue): D381–7. doi:10.1093/nar/gkr847. PMC 3245023. PMID 21993301.
  2. Polbase Reference List
  3. Polymerases in Polbase
  4. Polbase search
  5. Polbase references
  6. Authors in Polbase
  7. Polbase organism list
  8. NIH SBIR Grant ##1R44GM087021
  9. Polbase at DRAM Archived 2012-03-28 at the Wayback Machine
  10. Evolving Polymerases Conference 2010 Archived 2012-03-28 at the Wayback Machine
  11. Abstract from the ISMB Rocky 2010 Conferences
  12. Rocky 2010 conference schedule
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