The drug discovery process has been deeply transformed recently by the use of computational ligand-based or structure-based methods, helping the lead compounds identification and optimization, and finally the delivery of new drug candidates more quickly and at lower cost. Structure-based computational methods for drug discovery mainly involve ligand-protein docking and rapid binding free energy...

An essential requirement for theoretical protein structure prediction is an energy function that can discriminate the native from non-native protein conformations. To date most of the energy functions used for this purpose have been extracted from a statistical analysis of the protein structure database, without explicit reference to the physical interactions responsible for protein stability. ...

The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity. Starting from the open crystal structures, we have studied the gating mechanism of these channels by mol...

this paper investigates the mechanism of water transportation through aquaporin-4(aqp4) of ratbrain cells by means of molecular dynamics simulation with charmm software. the aqp4 wasembedded into a bilayer made of dimystroilphosphatylcholine (dmpc). the results illustrate thatwater molecules move through aqp4's channel with change of orientation of oxygen of eachwater molecule.

The interaction between proteins and membranes has an important role in biological pro-cesses.We have calculated energies of interaction between Melittin and DMPC bilayer in differenttemperatures. We have used the CHARMM software for MD simulation under the canonical (N,V, E) ensemble at different temperatures. The computations have shown that water moleculeshave more penetration into the bilay...