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3D-footprint (RRID:SCR_015713)


http://floresta.eead.csic.es/3dfootprint

Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.


Keywords

dna binding protein structure, protein data bank, sequencing, protein-dna interface

Resource ID

SCR_015713

Website Status

Last checked up

Resource Type

Resource, data or information resource, database

Funding Information

CSIC | 200720I038

Availability

Freely available, Free for academic use, Tutorial available

Proper citation

3D-footprint, RRID:SCR_015713

Terms of Use URLs

http://floresta.eead.csic.es/3dfootprint/credits.html

Reference

PMID:19767616

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Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch are assigned RRIDs which are used to cite resources in scientific manuscripts.

3D-footprint: a database for the structural analysis of protein-DNA complexes.

  • Contreras-Moreira B
  • Nucleic Acids Res.
  • 2010 Jan 22

3D-footprint is a living database, updated and curated on a weekly basis, which provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins that recognize a similar DNA motif and (iii) BLAST similar DNA-binding proteins, highlighting interface residues in the resulting alignments. Each complex in the database is dissected to draw interface graphs and footprint logos, and two complementary algorithms are employed to characterize binding specificity. Moreover, oligonucleotide sequences extracted from literature abstracts are reported in order to show the range of variant sites bound by each protein and other related proteins. Benchmark experiments, including comparisons with expert-curated databases RegulonDB and TRANSFAC, support the quality of structure-based estimates of specificity. The relevant content of the database is available for download as flat files and it is also possible to use the 3D-footprint pipeline to analyze protein coordinates input by the user. 3D-footprint is available at http://floresta.eead.csic.es/3dfootprint with demo buttons and a comprehensive tutorial that illustrates the main uses of this resource.

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