Lepšík M., Kříž Z., Havlas Z.:
Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations.
Proteins: Structure, Function and Genetics 57 (2): 279-293, 2004.

Zharov I., Weng T.-C., Orendt A.M., Barich D.H., Penner-Hahn J., Grant D.M., Havlas Z., Michl J.:
Metal cation-methyl interactions in CB11Me12- salts of Me3Ge+, Me3Sn+, and Me3Pb+.
Journal of the American Chemical Society 126 (38): 12033-12046, 2004.

Svozil D., Jungwirth P., Havlas Z.:
Electron binding to nucleic acid bases. Experimental and theoretical studies. A review.
Collection of Czechoslovak Chemical Communications 69 (7): 1395-1428, 2004.

Kleifeld O., Rulíšek L., Bogin O., Frenkel A., Havlas Z., Burstein Y., Sagi I.:
Higher metal-ligand coordination in the catalytic site of cobalt-substituted Thermoanaerobacter brockii alcohol dehydrogenase lowers the barrier for enzyme catalysis.
Biochemistry 43 (22): 7151-7161, 2004.