The structural impact of DNA mismatches.

The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produced significant local structural alterations, especially in the case of purine transversions. Mismatched pairs often show promiscuous hydrogen bonding patterns, which interchange among each other in the nanosecond time scale.

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations.

RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking methods are insufficient.

Localizing the Charged Side Chains of Ion Channels within the Crowded Charge Models.

The simplified coarse grained models of selectivity of Nonner and co-workers predict ion selectivity for a variety of different ion channels. The model includes the charged atoms of the channel's charged residues and permeant ions. However its MC implementation does not take advantage of the increasingly large body of structural information available.