Recent advances in implicit solvent-based methods for biomolecular simulations

J Chen, CL Brooks III, J Khandogin - Current opinion in structural biology, 2008 - Elsevier
J Chen, CL Brooks III, J Khandogin
Current opinion in structural biology, 2008Elsevier
Implicit solvent-based methods play an increasingly important role in molecular modeling of
biomolecular structure and dynamics. Recent methodological developments have mainly
focused on the extension of the generalized Born (GB) formalism for variable dielectric
environments and accurate treatment of nonpolar solvation. Extensive efforts in
parameterization of GB models and implicit solvent force fields have enabled ab initio
simulation of protein folding to native or near-native structures. Another exciting area that …
Implicit solvent-based methods play an increasingly important role in molecular modeling of biomolecular structure and dynamics. Recent methodological developments have mainly focused on the extension of the generalized Born (GB) formalism for variable dielectric environments and accurate treatment of nonpolar solvation. Extensive efforts in parameterization of GB models and implicit solvent force fields have enabled ab initio simulation of protein folding to native or near-native structures. Another exciting area that has benefited from the advances in implicit solvent models is the development of constant pH molecular dynamics methods, which have recently been applied to the calculations of protein pKa values and the studies of pH-dependent peptide and protein folding.
Elsevier
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