3D-footprint: DNA-binding protein database

What you can do:
Find information about the binding specificity of DNA-binding proteins.
  • 3D-footprint is a database 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.
  • 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.
  • DNA-protein interaction
  • DNA-binding proteins
  • transcription factor
  • structure-based binding specificity
  • binding specificity
  • protein binding specificity
This record last updated: 01-13-2010
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