3D-footprint -- database of DNA-binding protein structures
What you can do:
Find binding specificity information about DNA-protein complexes.
Highlights:
- 3D-footprint is a 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.
- 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.
Keywords:
- DNA-protein interaction
- DNA-protein comeplex
- DNA-protein structure
- binding specificity
Literature & Tutorials:
This record last updated: 12-1-2009