Sentence examples for simulations of proteins from inspiring English sources
MD simulations of proteins yield information on the relative stability and fluctuations of parts of the proteins.
The effectiveness of principal components analysis (PCA), an already established mathematical technique for finding global, correlated motions in atomic simulations of proteins, is evaluated here for coarse-grained trajectories.
This paper reviews the key issues involved in achieving ultra-strong scaling of methodologically correct biomolecular simulations, in particular, the treatment of the long range electrostatic forces present in simulations of proteins in water and membranes.
Utilizing atomistic level MD simulations of proteins or protein in association with other molecules (such as binding partners or enzyme-substrate complex) as input, this methodology pays close attention to the anharmonic nature of internal protein motions and pursues the higher-order statistics of the internal motions.
The parameters of protein residues were assigned on the basis of the AMBER ff03 force field, a point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
In this review, we emphasize on CG models developed for MD simulations of proteins and briefly mention lipid models that are comprehensively reviewed by Venturoli (Venturoli et al. 2006).
The partnership is intended to use a variant of the Blue Gene architecture that will enable a supercomputer to handle tasks beyond the biological simulations of protein folding.
Knowledge-based potentials are widely used in simulations of protein folding, structure prediction, and protein design.
Recent improvements in methodology and increased computer power now allow atomistic computer simulations of protein folding.
This new model allows the results from mesoscale simulations to be incorporated into micro- or macro-scale CFD transport simulations of protein adsorption in practical devices.
All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association.
