Predicting protein–DNA binding specificity is a challenging yet essential task for
understanding gene regulation. Protein–DNA complexes usually exhibit binding to a …

The double-stranded RNA-binding domain (dsRBD) is a common RNA-binding motif found
in many proteins involved in RNA maturation and localization. To determine how this …

Thermodynamic and kinetic analyses of biomolecular interactions reveal details of the
energetic and dynamic features of molecular recognition processes, and complement …

We developed a knowledge-based statistical energy function for protein− ligand, protein−
protein, and protein− DNA complexes by using 19 atom types and ad istance-scale f inite i …

Structural studies of protein-DNA complexes have shown that there are many distinct
families of DNA-binding proteins, and have shown that there is no simple “code” describing …

Intrinsic flexibility of DNA has hampered the development of efficient protein− DNA docking
methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing)[C …

Escherichia coli actively imports nickel via the ATP-dependent NikABCDE permease. NikR,
a protein of the ribbon-helix-helix family of transcription factors, represses expression of the …

To understand the role of aromatic–aromatic interactions in imparting specificity to the
folding process, the geometries of four aromatic residues with different sequence spacing …

Certain CRISPR-Cas elements integrate into Tn7-like transposons, forming CRISPR-
associated transposon (CAST) systems. How the activity of these systems is controlled in …

The proteins that bind double-helical DNA present various microenvironments that sense
and/or induce signals in the genetic material. The high-resolution structures of protein-DNA …