Recent advances in implicit solvent-based methods for biomolecular simulations.
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 pK(a) values and the studies of pH-dependent peptide and protein folding.
Chen
Jianhan
J
Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA.
Brooks
Charles L
CL
Khandogin
Jana
J
D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins; D012997:Solvents