Reference: Galper, A. R.; Millis, D. H.; & Brutlag, D. L. Knowledge-Based Simulation on DNA Metabolism: Prediction of Action and Envisionment of Pathways. 1990.
Abstract: Unlike intermediary metabolism, DNA metabolism is characterized by discrete, temporally ordered events, in which the concentrations of substrates are assumed to be sufficient to support metabolic reactions. We describe a knowledge-based, discrete-event simulation of DNA metabolism that can accurately predict the actions of enzymes under a large number of experimental conditions, and that can envision a subset of the possible metabolic pathways followed by substrates. We use a structural representation for substrates, and a functional representation for enzymes. The system is built in KEE (3.1.75), relying heavily on the truth-maintenance system for rapid inference and explanation. At present, we have modeled most of the major explanation. At present, we have modeled most of the major behaviors of E. coli DNA polymeras I and DNA ligase. The system is a first step toward building an interactive tool for reasoning about DNA metabolism.