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LM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction
Journal article   Open access   Peer reviewed

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

Zichen Wang, Steven A Combs, Ryan Brand, Miguel Romero Calvo, Panpan Xu, George Price, Nataliya Golovach, Emmanuel O Salawu, Colby J Wise, Sri Priya Ponnapalli, …
Scientific reports, v 12(1), pp 6832-6832
27 Apr 2022
DOI: https://doi.org/10.1038/s41598-022-10775-y
PMID: 35477726
Featured in Collection :   UN Sustainable Development Goals @ Drexel
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https://www.nature.com/articles/s41598-022-10775-y.pdfView
Published, Version of Record (VoR) Open
url
https://doi.org/10.1038/s41598-022-10775-yView
Published, Version of Record (VoR) Open

Abstract

Amino Acid Sequence Deep Learning Language Neural Networks, Computer Proteins - chemistry
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.

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53 citations in Web of Science
56 citations in Scopus

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Collaboration types
Industry collaboration
Domestic collaboration
Web of Science research areas
Biochemistry & Molecular Biology
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