Homopolymeric stretches of deoxyadenosine nucleotides (A's) on one strand of double-
stranded DNA, referred to as poly (dA: dT) tracts or A-tracts, are overabundant in eukaryotic …

We present a brief, and largely personal, history of computer simulations of DNA and RNA
oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both …

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 …

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important
role in many biological phenomena, roles that range from stabilization of biomolecular …

We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field,
where emphasis has been made on the correct representation of the α/γ concerted rotation …

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 …

Although molecular dynamics (MD) simulations have been used extensively to study the
structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based …

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 …

Over the past two decades, significant experimental advances have increased our ability to
control and manipulate individual DNA molecules. This capability has permitted …