CAVER: a new tool to explore routes from protein clefts, pockets and cavities. - Martin Petrek; Michal Otyepka; Pavel Banás; Pavlína Kosinová; Jaroslav Koca; Jirí Damborský (BMC Bioinform., 2006)

Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. - Pavel Banás; Michal Otyepka; Petr Jerábek; Martin Petrek; Jirí Damborský (J. Comput. Aided Mol. Des., 2006)

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)

Computational docking analysis on selective inhibition and binding affinity of synthetic inhibitors towards Matrix Metalloproteinase (MMPs) isoforms. - C. Sudandiradoss; Martin Petrek (IWBBIO, 2014)