… formed in the context of all possible nearest-neighbor base pairs. Current … to empirical
nearest-neighbor effects. Molecular dynamics simulations based on a molecular mechanic force …

… Here, we present a combined molecular dynamics/quantum … Crick base pairs. NN predictions
for Watson-Crick and modified … minimize the effects of terminal base pair dynamics and MD …

… possible Watson–Crick NN base pairs and two helix initiation … To understand the quantitative
impact of molecular crowding on … Molecular dynamic simulations have also shown that the …

… of effective base pairing and (nearest neighbor) base-pair … Molecular dynamics (MD)
simulations based on a molecular … the base-pair step contributions and do not consider effects due …

… base pairing can be determined by the summation of the free energy changes due to all
adjacent NN base pair … Therefore, problems arising in the stability prediction due to the effect of …

… opening-closing transition were obtained and the results at low forces were in good agreement
with the nearest-neighbor model. The temperature and force dependence of the opening …

… research, we combined measurements from UV melting experiments with molecular simulation
… of the two neighboring base pairs. ΔG 37,termAU represents the penalty for each A–U …

… One critical aspect of association kinetics that we did not study is the effect of mismatches.
A recent study investigated how single, double, and triple mismatches influence duplex …

… the central base pairs from the 5′ flanking base pair of G 1 to the 3′ flanking base pair
of … As discussed for AN dG, the most stabilizing effects occur for the next-nearest-neighbor …

… of force fields in molecular dynamics simulations. Our results … only involves consideration of
the base pairing, and this work … from previous data or nearest neighbor approximations, and …