Penicillin G acylases (PGAs) are enantioselective enzymes catalyzing a hydrolysis of stable amide bond in a broad spectrum of substrates. Among them, derivatives of α- and β-amino acids represent a class of compounds with high application potential. PGAEc from Escherichia coli and PGAA from Achromobacter sp. CCM 4824 were used to catalyze enantioselective hydrolyses of seven selected N-phenylacetylated α/β-amino acid racemates. The PGAA showed higher stereoselectivity for enantiomers of N-PhAc-β-homoleucine, N-PhAc-α-tert-leucine and N-PhAc-β-leucine. To study the mechanism of enantiodiscrimination on molecular level, we have constructed a homology model of PGAA that was used in molecular docking experiments with the same substrates. In-silico experiments successfully reproduced the data from experimental enzymatic resolutions confirming validity of employed modeling protocol. We employed this protocol to evaluate enantiopreference of PGAA towards seven new substrates with application potential. For five of them, high enantioselectivity of PGAA was predicted.