Long-timescale molecular dynamics simulations of protein structure and function.

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Virtual screening: an endless staircase? (2010, background): “In this respect, advanced and specialized computer hardware might enable extended (>100 ns) dynamics simulations of macromolecular targets and receptor–ligand complexes on a routine basis, which might help our understanding of allosteric effects and flexible fit phenomena of drug-like ligands and ef”
Discovery Through the Computational Microscope (2009, neutral): “Moreover, smaller systems have been simulated for 10–100 ms (Freddolino et al., 2008, 2009; Maragakis et al., 2008; Klepeis et al., 2009; Freddolino and Schulten, 2009).”
Systematic Validation of Protein Force Fields against Experimental Data (2012, background): “Historically, two principal factors have limited the utility of molecular dynamics (MD) simulations as a research tool in biology and biophysics [1].”
ACPYPE - AnteChamber PYthon Parser interfacE (2012, background): “Molecular Dynamics (MD) and NMR Structure Calculation software (NMRSC) have matured in line with these advances in MM to become more complex, faster and precise; MD and NMRSC software packages can now perform calculations that were previously thought to be very difficult to handle [4].”