Generative De Novo Protein Design with Global Context

Abstract

The linear sequence of amino acids determines protein structure and function. Protein design, known as the inverse of protein structure prediction, aims to obtain a novel protein sequence that will fold into the defined structure. Recent works on computational protein design have studied designing sequences for the desired backbone structure with local positional information and achieved competitive performance. However, similar local environments in different backbone structures may result in different amino acids, indicating that protein structure's global context matters. Thus, we propose the Global-Context Aware generative de novo protein design method (GCA), consisting of local and global modules. While local modules focus on relationships between neighbor amino acids, global modules explicitly capture non-local contexts. Experimental results demonstrate that the proposed GCA method outperforms state-of-the-arts on de novo protein design. Our code and pretrained model will be released.