title: Protein folding and unfolding by all-atom molecular dynamics simulations.
abstract: Computational protein folding can be classified into pathway and sampling approaches. Here, we use the AMBER simulation package as an example to illustrate the protocols for all-atom molecular simulations of protein folding, including system setup, simulation, and analysis. We introduced two traditional pathway approaches: ab inito folding and high-temperature unfolding. The popular replica exchange method was chosen to represent sampling approaches. Our emphasis is placed on the analysis of the simulation trajectories, and some in-depth discussions are provided for commonly encountered problems.
authors.affiliation: Genome Center, University of California, Davis, CA, USA.
authors.forename: Hongxing
authors.initials: H
authors.lastname: Lei
authors.forename: Yong
authors.initials: Y
authors.lastname: Duan
mesh_terms: D003198:Computer Simulation; D007700:Kinetics; D008968:Molecular Conformation; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013696:Temperature; D013816:Thermodynamics