Polbase (DNA Polymerase Database) is an open repository of

DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create t ...

information. Polbase captures information from published research on polymerase activity, and presents it in context with related work. Polbase indexes over 5,000 references 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.

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 * Search by author, organism, polymerase name, property, etc. * Browsing by reference * Browsing by author * Browsing by organism

Information sources

Polbase draws information from a variety of sources including

PubMed PubMed is an openly accessible, free database which includes primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institute ...

, PDB, and directly from polymerase investigators.

Interconnections

Polbase is connected with various other databases. These include: * The Protein Data Bank
European Bioinformatics Institute

ExPASy Bioinformatics Resource Portal
*

UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

BRENDA Brenda is a feminine given name in the English language. Origin The overall accepted origin for the female name Brenda is the Old Nordic male name ''Brandr'' meaning both ''torch'' and ''sword'': evidently the male name Brandr took root in areas ...

* Various Scientific Journals

History

Polbase began in March 2009 with a grant from the NIH's SBIR program and was first presented to the public at MIT's DNA and Mutagenesis Meeting In March 2010 Polbase was presented to a larger audience at the Evolving Polymerases 2010 Conference. Polbase was also presented in more technical detail at the Rocky 2010 ISMB Conference.Rocky 2010 conference schedule
/ref> Polbase is described in more detail in the 2012 Nucleic Acids Research Database Issue. Polbase was built at

New England Biolabs New England Biolabs (NEB) is an American life sciences company which produces and supplies recombinant and native enzyme reagents for life science research. It also provides products and services supporting genome editing, synthetic biology and ...

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

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External links

The DNA Polymerase Database (Polbase)
Enzyme databases DNA replication