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Publications
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Okumura,
H., E. Gallicchio, and R.M. Levy. Conformational populations of
ligand-sized molecules by replica exchange molecular dynamics
and temperature reweighting. J. Comp. Chem., (2009). In press.
Gallicchio,
E., K. Paris, and R.M. Levy. The AGBNP2 Implicit Solvent Model.
J. Chem. Theory & Comput., (2009) Article ASAP.
doi.10.1021/ct900234u
Zheng,
W., M. Andrec, E. Gallicchio, and R.M. Levy. Recovering Kinetics
from a Simplified Protein-Folding Model Using Replica Exchange
Simulations, a Kinetic Network and Effective Stochastic
Dynamics. J. Phys. Chem. B., (2009). In press.
Frenkel,
Y.V., E. Gallicchio, K. Das, R.M. Levy, and E. Arnold. Molecular
dynamics study of non-nucleoside HIV-1 RT inhibitor
TMC278/rilpivirine aggregates: correlation between amphiphilic
properties of the
drug and oral bioavailability. J. Med. Chem., in press.
Lapelosa,
M., E. Gallicchio, G. Ferstandig Arnold, E. Arnold and R.M.
Levy. In silico vaccine design based on molecular simulations of
rhinovirus chimeras presenting HIV-1 gp41 epitopes. J. Mol.
Biol., 385, 675-691 (2009). doi:10.1016/j.jmb.2008.10.089
Felts, A.K.,
M. Andrec, E. Gallicchio, and R.M. Levy. Protein Folding and
Binding: Effective Potentials, Replica Exchange Simulations, and
Network Models, in "Water and Biomolecules - Physical
Chemistry of Life Phenomena", Springer Science (2008).
Felts,
A.K., K. Paris, E. Gallicchio, R.A. Friesner, and R.M. Levy.
Predicting Long Loops with the AGBNP Implicit Solvent Model
using Hierarchical Torsion Angle Sampling and Protein Local
Optimization. J. Chem. Theor. Comp., 4, 855-858 (2008).
doi:10.1021/Fct800051k
Zheng,
W., M. Andrec, E. Gallicchio, and R.M. Levy. Simple Continuous
and Discrete Models for Simulating Replica Exchange Simulations
of Protein Folding. J.
Phys. Chem. B,
112,
6083-6093 (2008). doi:10.1021/jp076377+
Gallicchio,
E., R.M. Levy, and M. Parashar. Asynchronous Replica Exchange
for Molecular Simulations. J.
Comp. Chem.,
29, 788-794 (2008).
doi:10.1002/jcc.20839
Knight,
J.L., Z. Zhou, E. Gallicchio, D.M. Himmel, R.A. Friesner, E.
Arnold, and R.M. Levy. Exploring structural variability in X-ray
crystallographic models using protein local optimization by
torsion angle sampling. Acta.
Cryst.,
D64, 383-396 (2008).
doi:10.1107/S090744490800070X
Zheng,
W., M. Andrec, E. Gallicchio, and R.M. Levy. Simulating replica
exchange simulations of protein folding with a kinetic network
model. Proc.
Natl. Acad. Sci. USA,
104, 15340-15345 (2007). doi:10.1073/pnas.0704418104
Krishna
Pratap Ravindranathan, Emilio Gallicchio, Ann E. McDermott, and
Ronald M. Levy Conformational Dynamics of Substrate in the
Active Site of Cytochrome P450 BM-3/NPG Complex: Insights from
NMR Order Parameters. J. Am. Chem. Soc. 129,
474-475 (2007). doi:10.1021/ja0672371
Su,
Y., E. Gallicchio, K. Das, E. Arnold, and R.M. Levy. Linear
Interaction Energy (LIE) Models for Ligand Binding in Implicit
Solvent: Theory and Application to the Binding of NNRTIs to
HIV-1 Reverse Transcriptase, J.
Chem. Theory Comput., 3,
256-277
(2007).doi:10.1021/ct600258e
Ravindranathan,
K.P., E. Gallicchio, R.A. Friesner, A.E. McDermott, and R.M.
Levy. Conformational equilibrium of cytochrome P450 BM-3
complexed with N-Palmitoylglycine: A replica exchange molecular
dynamics study. J.
Am. Chem. Soc.,
128,
5786-5791 (2006).
doi:10.1021/ja058465i
Zhang,
L., M. Parashar, E. Gallichio and R.M. Levy. Salsa: Scalable
Asynchronous Replica Exchange for Parallel Molecular Dynamics
Applications. Proceedings of the 35th International Conference
on Parallel Processing (ICPP 2006), Columbus, OH, USA, IEEE
Computer Society Press, pp. 127 - 134, August 2006.
doi:10.1109/ICPP.2006.63
Ravindranathan,
K.P., E. Gallicchio, and R.M. Levy. Conformational Equilibria
and Free Energy Profiles for the Allosteric Transition of the
Ribose Binding Protein. J. Mol. Biol., 353,
196-210 (2005).doi:10.1016/j.jmb.2005.08.009
Banks,
J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K.
Felts, T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M.
Philipp, M.P. Repasky, L.Y. Zhang, B.J. Berne, R.A. Friesner, E.
Gallicchio, and R.M. Levy. Integrated Modeling Program, Applied
Chemical Theory (IMPACT). J. Comp. Chem., 26,
1752 (2005). http://dx.doi.org/10.1002/jcc.20292
Andrec,
M., A.K. Felts, E. Gallicchio, and R.M. Levy. Protein Folding
Pathways from Replica Exchange Simulations and a Kinetic Network
Model. Proceedings Natl. Acad. Sci. USA, 102,
6801-6806 (2005).http://dx.doi.org/10.1073/pnas.0408970102
Gallicchio,
E., M. Andrec, A.K. Felts, and R.M. Levy. Temperature Weighted
Histogram Analysis Method, Replica Exchange, and Transition
Paths. J. Phys. Chem. B, 109, 6722-6731
(2005).doi:10.1021/jp045294f
Felts,
A.K., Y. Harano, E. Gallicchio, R.M. Levy. Free energy
surfaces of beta-hairpin and alpha-helical peptides generated by
replica exchange molecular dynamics with the AGNP implicit
solvent model. PROTEINS: Structure, Function, and
Bioinformatics, 56,310-321 (2004).
doi:10.1002/prot.20104
Y.
Su and E. Gallicchio, The Non-polar Solvent Potential of Mean
Force for the Dimerization of Alanine Dipeptide: The Role of
Solute-Solvent van der Waals Interactions. Biophysical
Chemistry. 109:251-260 (2004).doi:10.1016/j.bpc.2003.11.007
Gallicchio
E., and R.M. Levy. AGBNP, an analytic implicit solvent
model suitable for molecular dynamics simulations and
high-resolution modeling, J. Comp. Chem. 25,
479-499 (2004).doi:10.1002/jcc.10400
R.
M. Levy, L. Y. Zhang, E. Gallicchio, A. K. Felts, On the
Non-Polar Hydration Free Energy of Proteins: Surface Area and
Continuum Solvent Models for the Solute-Solvent Interaction
Energy, J. Am. Chem. Soc., 125, 9523-9530 (2003).
Felts,
A.K., E. Gallicchio, A. Wallqvist, and R.M. Levy. Distinguishing
Native Conformations of Proteins from Decoys with an Effective
Free Energy Estimator based on the OPLS All-Atom Force Field and
the Surface Generalized Born Solvent Model. Proteins, 48,
404-422 (2002).
E.
Gallicchio, L.Y. Zhang, and R.M. Levy. The SGB/NP Hydration Free
Energy Model Based on the Surface Generalized Born Solvent
Reaction Field and Novel Non-Polar Hydration Free Energy
Estimators. J. Comp. Chem.,23, 517-529 (2002).
Wallqvist,
A., E. Gallicchio, A.K. Felts, and R.M. Levy. Detecting Native
Protein Folds Among Large Decoy Sets With the OPLS All-Atom
Potential and Surface Generalized Born Solvent Model, in
"Computational Methods for Protein Folding: A Special
Volume of Advances in Chemical Physics," Vol. 120, R.
Friesner, editor, I. Prigogine and S.A. Rice, series editors,
John Wiley & Sons, 459-486 (2002).
Wallqvist,
A., E. Gallicchio, and R.M. Levy. A Model for Studying Drying at
Hydrophobic Interfaces: Structural and Thermodynamic Properties.
J. Phys. Chem., 105, 6745-6753 (2001).
Felts,
A.K., A. Wallqvist, E. Gallicchio, D. Bassolino, S.R. Krystek
and R.M. Levy. Fold Recognition using the OPLS All-Atom
Potential and the Surface Generalized Born Solvent Model, in
"Lecture Notes in Computational Science and Engineering
(LNCSE)", Vol. 24, Springer-Verlag, Berlin, 2002.
Chernyavsky,
B., E. Gallicchio, D. Knight, R. Levy, and A. Page. The Rutgers
Computational Grid: A Distributed Linux PC Cluster.Â
Cluster Computing (2002)
Zhang,
L., E. Gallicchio, R. Friesner, and R.M. Levy. Solvent Models
for Protein-Ligand Binding: Comparison of Implicit Solvent
Poisson and Surface Generalized Born Models with Explicit
Solvent Simulations.J. Comp. Chem.,22, 591-607
(2001).
Gallicchio,
E., M. Kubo, and R.M. Levy. Enthalpy-Entropy and Cavity
Decomposition of Alkane Hydration Free Energies: Numerical
Results and Implications for Theories of Hydrophobic Solvation.
J. Phys. Chem., 104, 6271-6285 (2000).
Zhang,
L., E. Gallicchio, and R.M. Levy. Implicit Solvent Models for
Protein-Ligand Binding: Insights Based on Explicit Solvent
Simulations. AIP Conference Proceedings (Simulation and
Theory of Electrostatic Interactions in Solutions), 492,
451-472 (1999).
Matubayasi,
N., E. Gallicchio, and R.M. Levy. On the local and nonlocal
components of solvation thermodynamics and their relation to
solvation shell models. J. Chem. Phys., 109,
4864-4872 (1998).
Gallicchio,
E., M.M. Kubo, and R.M. Levy. Entropy-Enthalpy Compensation in
Solvation and Ligand Binding Revisited. J. Am. Chem Soc.,
120, 4526-4527 (1998).
Levy,
R.M., and E. Gallicchio. Computer Simulations with Explicit
Solvent: Recent Progress in the Thermodynamic Decomposition of
Free Energies, and in Modeling Electrostatic Effects.Annual
Review of Physical Chemistry,49, 531-567 (1998).
Kubo,
M.M., E. Gallicchio, and R.M. Levy. Thermodynamic Decomposition
of Hydration Free Energies by Computer Simulation: Application
to Amines, Oxides, and Sulfides. J. Phys. Chem., 101,
10527-10534 (1997).
E.
Gallicchio, S. A. Egorov and B. J. Berne. On the Application of
Numerical Analytic Continuation Methods to the Study of Quantum
Mechanical Vibrational Relaxation Processes'', J. Chem.
Phys., 109, 7745 (1998).
E.
Gallicchio, M. F. Kubo and R. M. Levy.Entropy-Enthalpy
Compensation in Solvation and Ligand Binding Revisited, J.
Am. Chem. Soc. , 120, 4526 (1998).
S.
A. Egorov, E. Gallicchio, B. J. Berne. The Simulation of the
Electronic Absorption Spectrum of a Chromophore Coupled to a
Condensed Phase Environment: Maximum Entropy Versus Singular
Value Decomposition Approaches, J. Chem. Phys., 107(22),
(1997).
E.
Gallicchio, B. J. Berne. On the Calculation of Dynamical
Properties of Solvated Electrons by Maximum Entropy Analytic
Continuation of Path Integral Monte Carlo data, J. Chem.
Phys.,105, 7064 (1996).
F.
Battaglia, T.F. George, E. Gallicchio. "Lezioni di Fisica
Classica e Quantistica'', CEDAM, Padova, Italy, 1996. pdf
E.
Gallicchio, B. J. Berne, ``The Absorption Spectrum of the
Solvated Electron in Fluid Helium by Maximum Entropy Inversion
of Imaginary Time Correlation Functions from Path Integral Monte
Carlo Simulations'', J. Chem. Phys., 101, 9909
(1994).
F.
Battaglia, E. Gallicchio.Thermodynamic Analysis of theÂ
vsÂ
Lattice Gases as Models for Molecular Adsorption on Surfaces, J.
Phys. Chem., 97, 6530 (1993).
E.
Gallicchio, F. Battaglia.FORTRAN Routine to Compute
Born-Oppenheimer Potential Energy Curves Directly from
Spectroscopic Data, J. Comput. Chem., 14, 579
(1993).
Ph.D. thesis:
``Quantum Dynamics in Condensed Phases by Maximum Entropy
Analytic Continuation of Euclidean Time Path Integrals'',
Graduate School of Arts and Sciences, Columbia University, New
York, 1996. pdf
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