Polbase
Encyclopedia
Polbase is an open repository of DNA polymerase
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.
entry. All information gathered in Polbase is linked to the original publication where it was reported.
, PDB
, and directly from polymerase investigators.
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.
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.
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
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)Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
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 PubMedPubMed
PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
, PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
, and directly from polymerase investigators.
Interconnections
Polbase is connected with various other databases. These include:- The Protein Data BankProtein Data BankThe Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
- European Bioinformatics Institute
- ExPASy Bioinformatics Resource Portal
- UniProtUniProtUniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...
- BRENDABRENDABRENDA is an enzyme information system representing one of the most comprehensive enzyme repositories.- Introduction :...
- PubMedPubMedPubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
- 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 MeetingIn 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.
Polbase is described in more detail in the 2012 Nucleic Acids Research Database Issue.
Polbase was built at New England Biolabs
New England Biolabs
New England Biolabs produces and supplies reagents for the life science industry. NEB offers 230 recombinant and 30 native restriction enzymes for genomic research, as well as nicking enzymes and DNA methylases. It offers products in the areas related to proteomics, DNA Sequencing, and drug...
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.