Co-evolution Transformer for Protein Contact Prediction

Proteins are the main machinery of life and protein functions are largely determined by their 3D structures. The measurement of the pairwise proximity between amino acids of a protein, known as inter-residue contact map, well characterizes the structural information of a protein. Protein contact prediction (PCP) is an essential building block of many protein structure related applications. The prevalent approach to contact prediction is based on estimating the inter-residue contacts using hand-crafted coevolutionary features derived from multiple sequence alignments (MSAs). To mitigate the information loss caused by hand-crafted features, some recently proposed methods try to learn residue co-evolutions directly from MSAs.