A-Prot: Protein structure modeling using MSA transformer

In this study, we propose a new protein 3D structure modeling method, A-Prot, using MSA Transformer, one of the state-of-the-art protein language models. For a given MSA, an MSA feature tensor and row attention maps are extracted and converted into 2D residue-residue distance and dihedral angle predictions. We demonstrated that A-Prot predicts long-range contacts better than the existing methods. Additionally, we modeled the 3D structures of the free modeling and hard template-based modeling targets of CASP14. The assessment shows that the A-Prot models are more accurate than most top server groups of CASP14. These results imply that A-Prot captures evolutionary and structural information of proteins accurately with relatively low computational cost. Thus, A-Prot can provide a clue for the development of other protein property prediction methods.