Abstract: In some embodiments, a method of determining a molecular structure of a protein is provided. A computing system receives voxel data representing electron density obtained via cryo-electron microscopy. The computing system uses one or more neural networks to predict one or more likelihoods for each voxel. The computing system determines a backbone structure based on the predicted likelihoods. The computing system maps amino acid sequences to the backbone structure based on the predicted likelihoods. Mapping the amino acid sequences to the backbone structure based on the predicted likelihoods includes conducting an alignment technique that uses a reward function and a gap penalty. The computing system determines locations of carbon, nitrogen, and oxygen atoms within the backbone structure based on the predicted likelihoods. The computing system determines side-chain atoms based on the predicted backbone structure and the amino acid sequences to complete the molecular structure.