Accurate prediction of protein function using statistics-informed graph networks

• Published in: Nature communications Vol. 15; no. 1; pp. 6601 - 12
• Main Authors: Jang, Yaan J., Qin, Qi-Qi, Huang, Si-Yu, Peter, Arun T. John, Ding, Xue-Ming, Kornmann, Benoît
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04.08.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/1305; 631/114/2397; 631/114/2410; 631/1647/48; 631/61/514/2008; Algorithms; Amino acid sequence; Annotations; Biotechnology; Computational Biology - methods; Couplings; Databases, Protein; Deep Learning; Drug development; Evolution; Functionals; Humanities and Social Sciences; Humans; Information processing; multidisciplinary; Networks; Proteins; Proteins - chemistry; Proteins - metabolism; Residues; Science; Science (multidisciplinary); Sequences; Statistics; Structure-function relationships
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-50955-0

Understanding protein function is pivotal in comprehending the intricate mechanisms that underlie many crucial biological activities, with far-reaching implications in the fields of medicine, biotechnology, and drug development. However, more than 200 million proteins remain uncharacterized, and computational efforts heavily rely on protein structural information to predict annotations of varying quality. Here, we present a method that utilizes statistics-informed graph networks to predict protein functions solely from its sequence. Our method inherently characterizes evolutionary signatures, allowing for a quantitative assessment of the significance of residues that carry out specific functions. PhiGnet not only demonstrates superior performance compared to alternative approaches but also narrows the sequence-function gap, even in the absence of structural information. Our findings indicate that applying deep learning to evolutionary data can highlight functional sites at the residue level, providing valuable support for interpreting both existing properties and new functionalities of proteins in research and biomedicine. Understanding protein function is vital for biomedicine. Here, authors develop a method using statistics-informed graph networks to predict functions from sequences. The method integrates evolutionary couplings and residue communities to improve the accuracy of function annotations for proteins.