Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. - Jan Kmunícek; Michal Bohác; Santos Luengo; Federico Gago; Rebecca C. Wade; Jirí Damborský (J. Comput. Aided Mol. Des., 2003)

Binding of Fatty Acids to beta-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants. - Petr Dobes; Jan Kmunícek; Vladimír Mikes; Jirí Damborský (J. Chem. Inf. Model., 2004)

Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services. - Ales Krenek; Martin Petrek; Jan Kmunícek; Jiri Filipovic; Zdenek Sustr; Frantisek Dvorák; Jirí Sitera; Jiri Wiesner; Ludek Matyska (PDP, 2008)