title: Molecular dynamics.
abstract: Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton's equations of motion. In this review, we present an overview of how the MD simulation can be conducted to address computational toxicity problems. The study cases will cover a standard MD simulation performed to investigate the overall flexibility of a cytochrome P450 (CYP) enzyme and a set of more advanced MD simulations to examine the barrier to ion conduction in a human α7 nicotinic acetylcholine receptor (nAChR).
authors.affiliation: Oak Ridge National Laboratory, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA. chengx@ornl.gov
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Cheng
authors.forename: Ivaylo
authors.initials: I
authors.lastname: Ivanov
mesh_terms: D019295:Computational Biology / Q000379:methods; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation; D011978:Receptors, Nicotinic / Q000737:chemistry; D012984:Software; D064569:alpha7 Nicotinic Acetylcholine Receptor
chemical_list: C579167:Chrna7 protein, human; D011978:Receptors, Nicotinic; D064569:alpha7 Nicotinic Acetylcholine Receptor; D003577:Cytochrome P-450 Enzyme System