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

ABSTRACT: 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 experimen

SUBMITTER: Contreras-Moreira B 

PROVIDER: S-EPMC2808867 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature