Abstract: An attention-based graph architecture that exploits MSA Transformer embeddings to directly produce models of three-dimensional folded structures from protein sequences includes a method and system for augmenting the protein sequence to obtain multiple sequence alignments, producing enriched individual and pairwise embeddings from the multiple sequence alignments using an MSA-Transformer, extracting relevant features and structure latent states from the enriched individual and pairwise embeddings for use by a downstream graph transformer, assigning individual and pairwise embeddings to nodes and edges, respectively, using the downstream graph transformer to operate on node representations through an attention-based mechanism that considers pairwise edge attributes to obtain final node encodings, and projecting the final node encodings to form the computer-modeled folded protein structure. An induced distogram of the computer-modeled folded protein structure may be computed.