Molecular dynamics (MD) simulations are useful tools for structure-based drug design. We review recent publications in which explicit solvent MD was used at the initial or final stages of high-throughput docking campaigns. In some cases, MD simulations of the protein target have been carried out before docking to generate a conformer of the protein which differs from the available crystal struc...

Molecular dynamics (MD) and binary collision approximation (BCA) computer simulations are employed to study surface damage by single ion impacts. The predictions of BCA and MD simulations of displacement cascades in amorphous and crystalline silicon and BCC tungsten by 1 keV Ar ion bombardment are compared. Single ion impacts are studied at angles of 50◦, 60◦ and 80◦ from normal incidence. Four...

The hydrophobic e ect of small apolar solutes is studied by molecular dynamic (MD) simulations. Interactions between two solutes can be described by the potential of mean force (PMF). The general feature of the PMF between two solutes in water is a potential barrier separating a stable contact con guration and a meta-stable solventseparated con guration. Interestingly, compared with classical M...

OBJECTIVE To develop a model to simulate visual fields (VFs) in glaucoma patients, and to characterize variability of the Mean Deviation (MD) VF summary measurement using real VFs and simulations. METHODS Pointwise VF variability was previously approximated using longitudinal VF data (24-2 SITA Standard, Humphrey Field Analyzer) from 2,736 patients; these data were used to build a non-paramet...

i The Soret circular dichroism (CD) spectrum of carbonmonoxy myoglobin dtifers strikingly for the two heme isomers: Aqzl =+90 M-’cm-’ for isomer A, AQ21 = -7 M-’cm-’ for isomer B (Aojula et al., BiochemJ. 250, 853(1988)). This observation implies significant differences in the protein conformation andlor distortions of the heme from planarity between the two isomers. Molecular dynamics simulati...

Surface tensions for liquid-vapor (lv), solid-liquid (sl), and solid-vapor (sv) interfaces are calculated from molecular dynamics simulations of the NaCl-water-air system. Three distinct calculation techniques based on thermodynamic properties are used to describe the multicomponent mixtures. Simulations of each bulk phase (including a liquid saturated solution) and various interfaces are carri...

Time-averaged restraints in molecular dynamics simulations offer a means to account for the averaging that is implicit in NMR spectroscopic data. We present a systematic investigation of the parameters which characterise time-averaged distance restraints. Using previously published data for a small protein, chymotrypsin inhibitor 2, we identify conditions which can lead to undesirable heating o...

Small- and wide-angle x-ray scattering (SWAXS) and molecular dynamics (MD) simulations are complementary approaches that probe conformational transitions of biomolecules in solution, even in a time-resolved manner. However, the structural interpretation of the scattering signals is challenging, while MD simulations frequently suffer from incomplete sampling or from a force-field bias. To combin...

Molecular Dynamics (MD) delivers dynamical information for large biomolecular systems using enormous CPU-resources. Consequently, several implementations of parallel MD programs have been presented. 1-13 We will analyse the characteristics of MD simulations of real-live biomolecular systems, summarise the serial algorithms tha t have been developed to significantly speed up these simulations an...

The in vitro study of membrane proteins for the purpose of physicochemical analysis or structure determination often relies upon successful reconstitution into detergent micelles. Moreover, a number of biological processes such as membrane protein folding and transport rely on lipid interactions which may resemble the micellar environment. Little is known about the structures of these micelles ...