With adoption of the petroleomics concept, significant effort has been made to create extensive databases of molecular structures and chemical and physical properties of complex petroleum mixtures. By collation of the available information provided by petroleomics, this study develops a new structure-based lumping kinetic model for hydrodesulfurization (HDS) of light gas oil. An advanced experimentation system, analytical technique, and computer software tool are employed to generate the necessary data. The model contains 16 structure-based lumps, each of which includes species having a similar structure and reactivity. The model allows for the tracking of changes in molecular structure type of the input and output mixtures during HDS. Its prediction capability is validated over a wide range of HDS operation temperatures (200-375 degrees C).