Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.

We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 μs of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al.

Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition.

Among numerous biological activities, natural polyphenols are antioxidants widely distributed in plants capable of inhibiting lipid peroxidation, which belongs to the most serious degenerative cell processes. Positioning of antioxidants in lipid bilayers can provide an insight to the lipid-peroxidation inhibition at the molecular level. This work aims at determining the location and orientation of quercetin and its most representative (glucuronidated, methylated, and sulfated) metabolites in lipid bilayer via molecular dynamic simulations.

Dimerisation process of silybin-type flavonolignans: insights from theory.

Natural polyphenols are known to be oxidized by free radicals, which partially explains the antioxidant properties of a number of these compounds. This oxidation may also be used to synthesise new compounds of biological interest, for example, dimers. The present theoretical study describes the existing experimental evidence showing that silybin and dehydrosilybin [natural polyphenols isolated from milk thistle (Silybum marianum)] form dimers regioselectively.

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.

We have developed an algorithm, "MOLE," for the rapid, fully automated location and characterization of molecular channels, tunnels, and pores. This algorithm has been made freely available on the Internet (http://mole.chemi.

CAVER: a new tool to explore routes from protein clefts, pockets and cavities.

Background: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent.

Results: The algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent.