LM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction

• Published in: Scientific reports Vol. 12; no. 1; pp. 6832 - 12
• Main Authors: Wang, Zichen, Combs, Steven A, Brand, Ryan, Calvo, Miguel Romero, Xu, Panpan, Price, George, Golovach, Nataliya, Salawu, Emmanuel O, Wise, Colby J, Ponnapalli, Sri Priya, Clark, Peter M
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 27.04.2022; Nature Publishing Group UK; Nature Portfolio
• Subjects: Amino Acid Sequence; Amino acids; Deep Learning; Drug development; Language; Neural networks; Neural Networks, Computer; Predictions; Protein engineering; Proteins; Proteins - chemistry
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-10775-y

Proteins perform many essential functions in biological systems and can be successfully developed as bio-therapeutics. It is invaluable to be able to predict their properties based on a proposed sequence and structure. In this study, we developed a novel generalizable deep learning framework, LM-GVP, composed of a protein Language Model (LM) and Graph Neural Network (GNN) to leverage information from both 1D amino acid sequences and 3D structures of proteins. Our approach outperformed the state-of-the-art protein LMs on a variety of property prediction tasks including fluorescence, protease stability, and protein functions from Gene Ontology (GO). We also illustrated insights into how a GNN prediction head can inform the fine-tuning of protein LMs to better leverage structural information. We envision that our deep learning framework will be generalizable to many protein property prediction problems to greatly accelerate protein engineering and drug development.