The B-form of DNA can populate two different backbone conformations: BI and BII, defined
by the difference between the torsion angles ε and ζ (BI= ε–ζ< 0 and BII= ε–ζ> 0). BI is the …

We have examined some subtle parameter modifications to the Cornell et al. force field,
which has proven quite successful in reproducing nucleic acid properties, but whose C2 …

Although nucleic acid structures are contained within the Protein Data Bank (PDB)(6) and
the Cambridge Structural Database (7), no single database is devoted entirely to nucleic …

The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator
protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by …

Nucleic acidparameters are developed for the all-atomempirical energy function used in the
CHARMM program. The parameters were determined by use of results for model …

The tetracycline repressor (TetR) regulates the most abundant resistance mechanism
against the antibiotic tetracycline in gram-negative bacteria. The TetR protein and its …

Molecular dynamic (MD) simulations using the BMS nucleic acid force field produce
environment and sequence dependent DNA conformations that closely mimic …

A generalized Born (GB) model has been applied to molecular dynamics simulations of the
A-and B-forms of a duplex DNA d (CCAACGTTGG) 2 and the corresponding duplex RNA r …

The hydroxyl radical footprint of the TATA-binding protein (TBP) bound to the high-affinity
sequence TATAAAAG of the adenovirus 2 major late promoter has been quantitatively …

Progress has recently been made towards the development of an accurate theoretical model
of DNA structure and motions on the basis of molecular dynamics computer simulations …