The ability to study "gain of function" mutations has important implications for identifying and mitigating risks to public health and national security associated with viral infections. Numerous respiratory viruses of concern have RNA genomes (e.g., SARS and flu). These RNA genomes fold into complex structures that perform several critical functions for viruses. However, our ability to predict the functional consequence of mutations in RNA structures continues to limit our ability to predict gain of function mutations caused by altered or novel RNA structures. Biological research in this area is also limited by the considerable risk of direct experimental work with viruses. Here we used small functional RNA molecules (ribozymes) as a model system of RNA structure and function. We used combinatorial DNA synthesis to generate all of the possible individual and pairs of mutations and used high-throughput sequencing to evaluate the functional consequence of each single- and double-mutant sequence. We used this data to train a machine learning model (Long Short-Term Memory). This model was also used to predict the function of sequences found in the genomes of mammals with three mutations, which were not in our training set. We found a strong prediction correlation in all of our experiments.