D.V. Makhov, A.A. Stuchebrukhov
An accurate and efficient procedure of fitting electric field potential by point charges
for QM/MM calculations.
Phys. Stat. Sol. (b), 243, 2030-2037, (2006).

D.M. Popovic, J. Quenneville, A.A. Stuchebrukhov
Combined DFT and Electrostatic Calculations of pKa’s in proteins: Study of Cytochrome c Oxidase.
Review article in: "Modern Methods for Theoretical Physical Chemistry of Biopolymers"
Editors: E.B. Starikow, J.P. Lewis, S. Tanaka, Elsevier 2006, [ISBN:0-444-52220-4].
(Chapter 3, pp 53-78)

A.A. Stuchebrukhov, D.M. Popovic
Comment on “Acidity of a Cu-bound Histidine in the Binuclear Center of Cytochrome c Oxidase”.
J. Phys. Chem. B, 110, 17286-17287, (2006).

D.V. Makhov, D.M. Popovic, A.A. Stuchebrukhov
Improved Density Functional Theory/Electrostatic Calculation of the His291 Protonation State in Cytochrome c Oxidase: Self-Consistent Charges for Solvation Energy Calculation.
J. Phys. Chem. B, 110, 12162-12166, (2006).

D.M. Popovic, A.A. Stuchebrukhov
Two Conformational States of Glu242 and pKa’s in Bovine Cytochrome c Oxidase.
Photochemical & Photobiological Sciences, 5, 611-620, (2006).

J. Quenneville, D.M. Popovic, A.A. Stuchebrukhov
Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase.
Biochim. Biophys. Acta - Bioenerg., 1757, 1035-1046, (2006).

D.M. Medvedev, E. Medvedev, A.A. Stuchebrukhov
Analysis of the kinetics of the membrane potential generated by cytochrome c oxidase
upon single electron injection.
Biochim. Biophys. Acta, 1710, 47-56, (2005).

D.M. Popovic, J. Quenneville, A.A. Stuchebrukhov
DFT/electrostatic calculations of pKa values in cytochrome c oxidase.
J. Phys. Chem. B, 109, 3616-3626, (2005).

D.M. Popovic, A.A. Stuchebrukhov
Proton Exit Channels in Bovine Cytochrome c Oxidase.
J. Phys. Chem. B, 109, 1999-2006, (2005).

M. Tashiro, A.A. Stuchebrukhov
Thermodynamic Properties of Internal Water Molecules in the Hydrophobic Cavity
around the Catalytic Center of Cytochrome c Oxidase.
J. Phys. Chem. B, 109, 1015-1022, (2005).

J. Quenneville, D.M. Popovic, A.A. Stuchebrukhov
Redox-Dependent pKa of CuB Histidine Ligand in Cytochrome c Oxidase.
J. Phys. Chem. B, 108, 18383-18389, (2004).

D.M. Popovic, A.A. Stuchebrukhov
Proton pumping mechanism and catalytic cycle of cytochrome c oxidase:
Coulomb pump model with kinetic gating.
FEBS Lett., 566, 126-130, (2004).

D.M. Popovic, A.A. Stuchebrukhov
Electrostatic study of proton pumping mechanism in cytochrome oxidase.
J. Am. Chem. Soc., 126, 1858-1871, (2004).

X. Zheng, D.M. Medvedev, J.Swanson, A.A. Stuchebrukhov
Computer simulations of internal water in cytochrome oxidase.
Biochim. Biophys. Acta, 1557, 99-107, (2003).

A.A. Stuchebrukhov
Coupled electron and proton transfer reactions. Proton pumps, cytochrome oxidase,
and biological energy transduction.
J.Theor.Comp.Chem., 1, 91-118, (2003), Review Article.

Yu. Georgievskii, E.S. Medvedev, and A.A. Stuchebrukhov
Theoretical Analysis of the Redox-Coupled Protonation of Heme a and CuA in the Cytochrome c Oxidase with CO-Inhibited Binuclear Center.
BioOrg. Chem. (Russ), 29, 21-29, (2003).

A.I. Kotelnikov, E.S. Medvedev, D.M. Medvedev, and A.A. Stuchebrukhov
Kinetic treatment of coupled electron and proton transfer in flash-photolysis experiments
on carbon monoxide-inhibited mixed-valence cytochrome c oxidase.
J. Phys. Chem. B,  105, 5789-5796, (2001).

D.M. Medvedev, I. Daizadeh, and A.A. Stuchebrukhov,
Electron transfer tunneling pathways in bovine heart cytochrome c oxidase.
J. Am. Chem. Soc., 122, 6571, (2000).

COMPLETE LIST OF PUBLICATIONS (1981-...)