- U. Bren, M. Hodo"s"cek, J. Koller,
Development and Validation of Empirical Force Field Parameters
for Netropsin,
J. Chem. Inf. Model., 45 (2005) 1546-1552.
- U. Bren, M. Zupan, F. P. Guengerich, J. Mavri,
Chemical Reactivity as a Tool to Study Carcinogenicity:
Reaction between Chloroethylene Oxide and Guanine,
J. Org. Chem., 71 (2006) 4078-4084.
- U. Bren, V. Martinek, J. Florian,
Decomposition of the Solvation Free Energies of Deoxyribonucleoside
Triphosphates Using the Free Energy Perturbation Method,
J. Phys. Chem. B, 110 (2006) 12782-12788.
- U. Bren, V. Martinek, J. Florian,
Free Energy Simulations of Uncatalyzed DNA Replication Fidelity:
Structure and Stability of T-G and dTTP-G Terminal DNA Mismatches
Flanked by a Single Dangling Nucleotide,
J. Phys. Chem. B, 110 (2006) 10557-10566.
- M. Bren, J. Florian, J. Mavri, U. Bren,
Do All Pieces Make a Whole?
Thiele Cumulants and the Free Energy Decomposition,
Theor. Chem. Acc., 117 (2007) 535-540.
- U. Bren, F. P. Guengerich, J. Mavri,
Guanine Alkylation by the Potent Carcinogen Aflatoxin B1:
Quantum Chemical Calculations,
Chem. Res. Toxicol., 20 (2007) 1134-1140.
- V. Martinek, U. Bren, M. F. Goodman, A. Warshel, J. Florian,
DNA Polymerase [Beta] Catalytic Efficiency Mirrors the Asn279-dCTP H-bonding Strength,
FEBS Lett., 581 (2007) 775-780.
- U. Bren, A. Kr"zan, J. Mavri,
Microwave Catalysis through Rotationally Hot Reactive Species,
J. Phys. Chem. A, 112 (2008) 166-171.
- K. Gale"sa, U. Bren, A. Kranjc, J. Mavri,
Carcinogenicity of Acrylamide: A Computational Study,
J. Agric. Food Chem., 56 (2008) 8720-8727.
- A. Perdih, U. Bren, T. "Solmajer,
Binding Free Energy Calculations of N-Sulphonyl-Glutamic Acid
Inhibitors of MurD Ligase,
J. Mol. Model., 15 (2009) 983-996.
- K. L. Brown, U. Bren, M. P. Stone, F. P. Guengerich,
Inherent Stereospecificity in the Reaction of Aflatoxin B1
8,9-Epoxide with Deoxyguanosine and Efficiency of DNA Catalysis,
Chem. Res. Toxicol., 22 (2009) 913-917. Selected as highlight of month May and included in the thematic collection Chemistry and Biology of DNA Damage .
- H. Zhang, U. Bren, I. D. Kozekov, C. J. Rizzo, D. F. Stec,
F. P. Guengerich,
Steric and Electrostatic Effects at the C2 Atom Substituent
Influence Replication and Miscoding of the DNA Deamination Product
Deoxyxanthosine and Analogs by DNA Polymerases,
J. Mol. Biol., 392 (2009) 251-269.
- T. Udommaneethanakit, T. Rungrotmongkol, U. Bren, V. Frecer,
S. Miertus,
Dynamic Behavior of Avian Influenza A Virus Neuraminidase Subtype
H5N1 in Complex with Oseltamivir, Zanamivir, Peramivir, and Their
Phosphonate Analogues,
J. Chem. Inf. Model., 49 (2009) 2323-2332.
- U. Bren, J. Lah, M. Bren, V. Martinek, J. Florian,
DNA Duplex Stability: The Role of Preorganized Electrostatics,
J. Phys. Chem. B, 114 (2010) 2876-2885.
- M. Bren, D. Jane"zi"c, U. Bren,
Microwave Catalysis Revisited: An Analytical Solution,
J. Phys. Chem. A, 114 (2010) 4197-4202.
- U. Bren, C. Oostenbrink,
Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand
Cooperativity Using Molecular Dynamics Simulations and Free-Energy
Calculations,
J. Chem. Inf. Model., 52 (2012) 1573-1582.
- U. Bren, D. Jane"zi"c,
Individual Degrees of Freedom and the Solvation Properties of Water,
J. Chem. Phys., 137 (2012) 024108.
- M. M. H. Graf, U. Bren, D. Haltrich, C. Oostenbrink,
Molecular Dynamics Simulations Give Insight into D-Glucose Dioxidation at C2 and C3 by Agaricus
Meleagris Pyranose Dehydrogenase,
J. Comput. Aided Mol. Des., 27 (2013) 295-304.
- T. Udommaneethanakit, T. Rungrotmongkol, P. Seneci, V. Frecer,
S. Miertus, U. Bren,
Drugs against Avian Influenza A Virus: Design of Novel Sulfonate Inhibitors of Neuraminidase N1,
Curr. Pharm. Des., in press 2013.
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