Publications

Full publication list is available at Google scholar

Selected publications

Protein pKa prediction by tree-based machine learning
AY Chen, J Lee, A Damjanovic, BR Brooks
Journal of Chemical Theory and Computation, in press

Determinants of conductance of a bacterial voltage-gated sodium channel
AY Chen, BR Brooks, A Damjanovic
Biophysical Journal, 120 (15), 3050-3069, 2021

Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions
A Damjanovic, AY Chen, RL Rosenberg, DR Roe, X Wu, BR Brooks
Proteins: Structure, Function, and Bioinformatics 88 (3), 527-539, 2020

Reservoir pH replica exchange
A Damjanovic, BT Miller, A Okur, BR Brooks
The Journal of Chemical Physics 149 (7), 072321, 2018

Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method
J Lee, BT Miller, A Damjanovic, BR Brooks
Journal of chemical theory and computation 11 (6), 2560-2574 2015

Constant pH molecular dynamics in explicit solvent with enveloping distribution sampling and Hamiltonian exchange
J Lee, BT Miller, A Damjanovic, BR Brooks
Journal of chemical theory and computation 10 (7), 2738-2750 (2014)

pH replica‐exchange method based on discrete protonation states
SG Itoh, A Damjanović, BR Brooks
Proteins: Structure, Function, and Bioinformatics 79 (12), 3420-3436 (2011)

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins
A Damjanovic, BR Brooks, B García-Moreno E
The Journal of Physical Chemistry A 115 (16), 4042-4053 (2011)

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study
A Damjanović, X Wu, BR Brooks
Biophysical journal 95 (9), 4091-4101 (2008)

Molecular dynamics study of water penetration in staphylococcal nuclease
A Damjanović, B García‐Moreno, EE Lattman, AE García
Proteins: Structure, Function, and Bioinformatics 60 (3), 433-449 (2005)

Chlorophyll Excitations in Photosystem I of Synechococcus elongatus
A Damjanović, HM Vaswani, P Fromme, GR Fleming
The Journal of Physical Chemistry B 106 (39), 10251-10262 (2002)

Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry, and polaron model study
A Damjanović, I Kosztin, U Kleinekathöfer, K Schulten
Physical Review E 65 (3), 031919 (2002)

Excitation transfer in the peridinin-chlorophyll-protein of Amphidinium carterae
A Damjanović, T Ritz, K Schulten
Biophysical journal 79 (4), 1695-1705 (2000)

Energy transfer between carotenoids and bacteriochlorophylls in light-harvesting complex II of purple bacteria
A Damjanović, T Ritz, K Schulten
Physical Review E 59 (3), 3293 (1999)

Pigment organization and transfer of electronic excitation in the photosynthetic unit of purple bacteria
X Hu, T Ritz, A Damjanović, K Schulten
The Journal of Physical Chemistry B 101 (19), 3854-3871 (1997)