The interaction of small molecules with DNA plays an essential role in many biological
processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study …

Classical atomistic simulations, also known as molecular mechanics simulations, use simple
potential-energy functions to model molecular systems at the atomic level. In this …

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …

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 describe Curves+, a new nucleic acid conformational analysis program which is
applicable to a wide range of nucleic acid structures, including those with up to four strands …

Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales
are critical for understanding macromolecular functioning. Coarse-grained representations …

We present the results of microsecond molecular dynamics simulations carried out by the
ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct …

It is well recognized that base sequence exerts a significant influence on the properties of
DNA and plays a significant role in protein–DNA interactions vital for cellular processes …

Curves+, a revised version of the Curves software for analyzing the conformation of nucleic
acid structures, is now available as a web server. This version, which can be freely accessed …

It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …