In silico methods and tools for drug discovery
In the past, conventional drug discovery strategies have been successfully employed to
develop new drugs, but the process from lead identification to clinical trials takes more than …
develop new drugs, but the process from lead identification to clinical trials takes more than …
Molecular dynamics simulations and drug discovery
This review discusses the many roles atomistic computer simulations of macromolecular (for
example, protein) receptors and their associated small-molecule ligands can play in drug …
example, protein) receptors and their associated small-molecule ligands can play in drug …
[HTML][HTML] Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
The introduction of accelerator devices such as graphics processing units (GPUs) has had
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …
Rational design of particle mesh Ewald compatible Lennard-Jones parameters for+ 2 metal cations in explicit solvent
Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD)
simulations on these systems require a validated set of parameters. Although there are more …
simulations on these systems require a validated set of parameters. Although there are more …
Implementing molecular dynamics on hybrid high performance computers–short range forces
The use of accelerators such as graphics processing units (GPUs) has become popular in
scientific computing applications due to their low cost, impressive floating-point capabilities …
scientific computing applications due to their low cost, impressive floating-point capabilities …
General purpose molecular dynamics simulations fully implemented on graphics processing units
Graphics processing units (GPUs), originally developed for rendering real-time effects in
computer games, now provide unprecedented computational power for scientific …
computer games, now provide unprecedented computational power for scientific …
GPU-accelerated molecular modeling coming of age
Graphics processing units (GPUs) have traditionally been used in molecular modeling solely
for visualization of molecular structures and animation of trajectories resulting from …
for visualization of molecular structures and animation of trajectories resulting from …
Accelerating molecular modeling applications with graphics processors
Molecular mechanics simulations offer a computational approach to study the behavior of
biomolecules at atomic detail, but such simulations are limited in size and timescale by the …
biomolecules at atomic detail, but such simulations are limited in size and timescale by the …
GPU accelerated Monte Carlo simulation of the 2D and 3D Ising model
The compute unified device architecture (CUDA) is a programming approach for performing
scientific calculations on a graphics processing unit (GPU) as a data-parallel computing …
scientific calculations on a graphics processing unit (GPU) as a data-parallel computing …
High-throughput sequence alignment using Graphics Processing Units
Background The recent availability of new, less expensive high-throughput DNA sequencing
technologies has yielded a dramatic increase in the volume of sequence data that must be …
technologies has yielded a dramatic increase in the volume of sequence data that must be …