Publications
H. A. Stern, "Coarse-grained and multiscale models of lipid
bilayers," in Multiscale Modeling of Particle
Interactions: Applications in Biology and
Nanotechnology, edited by D. J. Gee and M. R. King,
Wiley, Hoboken, to appear.
C. Gao, M.-S. Park, and H. A. Stern, "Accounting for ligand
conformational restriction in calculations of
protein-ligand binding affinities," Biophys J.,
accepted.
A. V. Smrcka, N. Kichik, T. Tarragó, M. Burroughs, M.-S.
Park, N. K. Itoga, H. A. Stern, B. M. Willardson, and E.
Giralt, "NMR analysis of G protein βγ subunit
complexes reveals a dynamic Gα-Gβγ
subunit interface and multiple protein recognition models,"
Proc. Nat. Acad. Sci. USA, in press.
I. Yildirim and H. A. Stern
and J. Sponer and N. Spackova and D. H. Turner,
"Effects of restrained sampling space and
nonplanar amino groups on free-energy predictions for
RNA with imino and sheared tandem GA base pairs flanked
by GC, CG, iGiC, or iCiG base pairs,"
J. Chem. Theory.
Comput. 5, 2088 (2009)
M.-S. Park, A. L. Dessal, A. V. Smrcka, and H. A. Stern,
"Evaluating docking methods for prediction
of binding affinities of small molecules to the G
protein βγ subunits," J. Chem. Inf.
Model, 49, 437 (2009)
H. A. Stern and K. G. Calkins, "On mesh-based Ewald methods: Optimal
parameters for two differentiation schemes,"
J. Chem. Phys. 128, 214106
(2008) erratum
C. Gao and H. A. Stern, "Scoring function accuracy for membrane
protein structure prediction," Proteins:
Struct., Funct., Genet. 68, 67
(2007)
H. A. Stern, "Molecular simulation with variable
protonation states at constant pH," J. Chem.
Phys. 126, 164112 (2007) erratum
R. Vargas, J. Garza, R.A. Friesner, H. A. Stern, B. P. Hay,
and D. A. Dixon, "Reply to comment on 'Strength of the
N–H...O=C and C–H...O=C bonds in formamide and
N-methylacetamide dimers' ", J. Phys. Chem.
A 109, 6991 (2005)
H. A. Stern, "A simple algorithm for isothermal-isobaric
molecular dynamics," J. Comp. Chem.
25, 749 (2004)
G. A. Kaminski and H. A. Stern and B. J. Berne and R. A.
Friesner, "Development of an accurate and robust
polarizable molecular mechanics force field from ab
initio quantum chemistry," J. Phys. Chem.
A 108, 621 (2004)
R. Elber, A. Càrdenas, A. Ghosh, H. A. Stern, "Bridging the
gap between long time trajectories and reaction pathways,"
Adv. Chem. Phys. 126, 93 (2003)
H. A. Stern and S. E. Feller, "Calculation of the dielectric permittivity
profile for a nonuniform system: Application to a
lipid bilayer simulation," J. Chem. Phys.
118, 3401 (2003)
H. Xu, H. A. Stern, B. J. Berne, "Can water polarizability be ignored in
hydrogen bond kinetics?", J. Phys. Chem.
B 106, 2054 (2002)
G. A. Kaminski, H. A. Stern, B. J. Berne, R. A. Friesner,
Y. X. Cao, R. B. Murphy, R. Zhou, T. A. Halgren,
"Development of a polarizable force field
for proteins via ab initio quantum chemistry: First
generation model and gas phase tests," J.
Comp. Chem. 23, 1515 (2002)
C. J. Margulis, H. A. Stern, B. J. Berne, "Helix unfolding and intramolecular
hydrogen bond dynamics in small alpha helices in
explicit solvent," J. Phys. Chem. B
106, 10748 (2002)
C. J. Margulis, H. A. Stern, B. J. Berne, "Computer simulation of a `green chemistry'
room-temperature ionic solvent," J. Phys.
Chem. B 106, 12017 (2002)
H. A. Stern, B. J. Berne, "Quantum effects in liquid water:
Path-integral simulations of a flexible and
polarizable ab initio model," J. Chem.
Phys. 115, 7622 (2001)
H. A. Stern, F. Rittner, B. J. Berne and R. A. Friesner,
"Combined fluctuating charge and
polarizable models: Application to a five-site water
potential function," J. Chem. Phys.
115, 2237 (2001)
R. Vargas, J. Garza, R. A. Friesner, H. A. Stern, B. P.
Hay, D. A. Dixon, "Strength of the N-H...O=C and C-H...O=C
bonds in formamide and N-methylacetamide dimers,"
J. Phys. Chem. A 105, 4963
(2001)
H. A. Stern, G. A. Kaminski, J. L. Banks, R. Zhou, B. J.
Berne and R. A. Friesner, "Fluctuating charge, polarizable dipole,
and models: Parameterization from ab initio quantum
chemistry," J. Phys. Chem. B.
103, 4730 (1999)