Our research focuses on atomic-detail computer simulation to examine problems in biochemistry
and structural biology. A particular interest is modeling proteins involved in cellular signal
transduction. We are investigating the ability of scoring functions based on crystal structures of
water-soluble proteins to identify native structures of membrane proteins, and the ability of mixed
quantum mechanical/classical mechanical calculations to reproduce spectra for different conformational
states of rhodopsin and other opsin pigments. We are also working to improve simulations with more
accurate potential energy functions, a rigorous treatment of changes in protonation state, incorporation
of quantum statistics of nuclear motion, and faster calculation of electrostatic forces.
Figure 1: Crystal Structure of rhodopsin Palczewski et al.,
Science 289, 739-745, (2000)
Relevant Publications
Gao C., Stern, H. A.
"Scoring function accuracy for membrane protein structure prediction,"
Proteins
2006,
in press
Stern, H. A.
"A simple algorithm for isothermal-isobaric molecular dynamics,"
J. Comp. Chem.
2004,
25,
749.
Kaminski, G. A., Stern, H. A., Berne, B. J., Friesner, R. A.
"Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry,"
J. Phys. Chem. A
2004,
108,
621.
Stern, H. A., Feller, S. E.
"Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation,"
J. Chem. Phys.
2003,
118,
3401.
Margulis, C. J., Stern, H. A., Berne, B. J.
"Helix unfolding and intramolecular hydrogen bond dynamics in small alpha helices in explicit solvent,"
J. Phys. Chem. B
2002,
106,
10748.
Stern, H. A., Rittner, F., Berne, B. J., Friesner, R. A.
"Combined fluctuating charge and polarizable models: Application to a five-site water potential function,"
J. Chem. Phys.
2001,
115,
7622.
Stern, H. A., Berne, B. J.
"Quantum effects in liquid water: Path-integral simulations of a flexible and polarizable ab initio model,"
J. Chem. Phys.
2001,
115,
7622.
