Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understanding metabolism is crucial to elucidate the fundamental principles of biology, and further to enable us to redesign it for the sustainable, biosynthetic pro-duction of bio-based fuels, commodity chemicals and medicines. Mathematical mod-els are essential to organize and understand the complexity of metabolism. They usu-ally represent metabolism as a network of reactions, but they tend to neglect the exact molecular structure of the metabolites. To redesign metabolic reactions, how-ever, a mechanistic understanding of metabolic reactions and their catalysts, proteins called enzymes, is essential. In this work, a mathematical description of enzymatic reaction mechanism, called generalized reaction rules, is applied to computationally simulate and predict meta-bolic processes at the level of atoms. Each reaction rule describes the catalytic activi-ty of an enzyme, or a group of enzymes, at the mechanistic level by encoding the re-arrangement of atoms in the reaction. The reaction rules are called “generalized”, because they mimic the ability of a single enzyme to catalyze multiple reactions by acting on a range of substrates. Using these reaction rules, we first developed a computational representation of me-tabolism that allowed tracking single atoms throughout complex metabolic reaction networks. The principle of atom-tracking was then used to develop a graph-theory based method to represent and analyze metabolic networks, and to reliably identify of metabolic pathways for the biosynthesis of chemicals. Next, we applied the gener-alized reaction rules to predict all possible novel, hypothetical reactions from known biological compounds, and we stored the five million generated novel reactions them in a database called ATLAS. Finally, the developed tools and resources were applied to specific engineering and research problems, such as the biosynthetic pathway design for the biofuel bisabolene and the plastic precursor 1,4-butanediol. We further pre-dicted a biosynthesis route for the pharmaceutical tetrahydropalmatine and engi-neered a yeast strain to produce it. Finally, we show that our tools can be used to mine available genome sequences to find organisms that can degrade xenobiotics. Our findings suggest that the atom-level representation of metabolism can greatly contribute to its understanding, exploration and prediction. Given the complexity of atom-level modeling of metabolic processes, we propose metrics that can approxi-mate the atom-level information to conserve the information at the level of big, hy-pothetical metabolic networks like ATLAS. This database plus the developed pathway search techniques form a valuable resource for scientist to help characterizing un-known biosynthesis pathways towards secondary metabolites, and for metabolic engi-neers for designing novel bioproduction pathways for chemicals. Hopefully, these considerations will contribute to a better understanding of metabolism, advance the exploration of the bioproduction of drugs and other valuable molecules, and acceler-ate metabolic engineering efforts to realize the switch from a petroleum-based chem-ical industry towards a more sustainable, bio-based production of society’s chemical needs.