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Database Commons - ZiFDB

ZiFDB

Citations: 73

z-index 0.00

Short name ZiFDB
Full name Zinc Finger Database
Description ZiFDB is a web-accessible database that houses information on individual C2H2 zinc fingers (ZFs) and engineered zinc finger arrays (ZFAs).
URL http://zifdb.msi.umn.edu
Year founded 2008
Last update & version NA    v2.0
Availability Not Available
University/Institution hosted University of Minnesota
Address 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
City Minneapolis
Province/State MN
Country/Region United States
Contact name Daniel F. Voytas
Contact email voytas@umn.edu
Data type(s)
Major organism(s)
Keyword(s)
  • C2H2 zinc finger
  • zinc finger array
Publication(s)
  • Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C?H? zinc fingers and engineered zinc finger arrays. [PMID: 23203887]

    Fengli Fu, Daniel F Voytas
    Nucleic acids research 2013:41(Database issue)
    10 Citations (Google Scholar as of 2016-01-19)

    Abstract: ZiFDB (Zinc Finger Database, http://zifdb.msi.umn.edu) is a web-accessible database that houses information on individual C(2)H(2) zinc fingers (ZFs) and engineered zinc finger arrays (ZFAs). ZiFDB serves as a resource for biologists interested in engineering ZFAs for use as sequence-specific DNA-binding reagents. Here, we describe four new features of ZiFDB: (i) the database allows users to input new ZFs and ZFAs; (ii) a shadow database temporarily stores user-submitted data, pending approval by the database curator and subsequent loading into the persistent database; (iii) ZiFDB contains 181 Context-Dependent Assembly (CoDA) ZFAs, which were generated by this newly described ZFA engineering platform; and (iv) the database also now contains 319 F1F2 CoDA units and 334 F2F3 CoDA units that can be used to construct CoDA arrays. In total, the new release of ZiFDB contains 1226 ZFs and 1123 ZFAs.

  • Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. [PMID: 18812396]

    Fengli Fu, Jeffry D Sander, Morgan Maeder, Stacey Thibodeau-Beganny, J Keith Joung, Drena Dobbs, Leslie Miller, Daniel F Voytas
    Nucleic acids research 2009:37(Database issue)
    63 Citations (Google Scholar as of 2016-01-19)

    Abstract: Zinc fingers are the most abundant DNA-binding motifs encoded by eukaryotic genomes and one of the best understood DNA-recognition domains. Each zinc finger typically binds a 3-nt target sequence, and it is possible to engineer zinc-finger arrays (ZFAs) that recognize extended DNA sequences by linking together individual zinc fingers. Engineered zinc-finger proteins have proven to be valuable tools for gene regulation and genome modification because they target specific sites in a genome. Here we describe ZiFDB (Zinc Finger Database; http://bindr.gdcb.iastate.edu/ZiFDB), a web-accessible resource that compiles information on individual zinc fingers and engineered ZFAs. To enhance its utility, ZiFDB is linked to the output from ZiFiT--a software package that assists biologists in finding sites within target genes for engineering zinc-finger proteins. For many molecular biologists, ZiFDB will be particularly valuable for determining if a given ZFA (or portion thereof) has previously been constructed and whether or not it has the requisite DNA-binding activity for their experiments. ZiFDB will also be a valuable resource for those scientists interested in better understanding how zinc-finger proteins recognize target DNA.

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Tags

Protein
Eukaryota
C2H2 zinc finger zinc finger array

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lina Ma [2016-09-26]
    • Hongyan Yin [2016-03-29]
    • Mengwei Li [2016-02-13]
    • Zhang Zhang [2016-01-19]
    • Hongyan Yin [2015-11-25]
    • Hongyan Yin [2015-06-26]
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