AI-driven approach reveals hidden protein relationships

In a recently published article in Nature Communications, a team of researchers from the University of Virginia -; including Phil Bourne, dean of the School of Data Science, Cam Mura, a senior scientist with the School, and Eli Draizen, a recent UVA alumnus-; offer an AI-driven approach to explore structural similarities and relationships across the protein universe.

Specifically, the authors report a computational framework that can detect and quantify such protein relationships at scale (across myriad proteins), in a novel, flexible, and nuanced manner that combines deep learning-based approaches with a new conceptual model, known as the Urfold, that allows for two proteins to exhibit architectural similarity despite having differing topologies or "folds."

The publication is the culmination of years of work by the Bourne Lab to develop this AI-driven framework, called DeepUrfold, to enable the Urfold theory of structure relationships to be explored systematically and at scale.

Bourne, founding dean of the School of Data Science, is world renowned in the scientific community for his research, including structural bioinformatics and computational biology more broadly. Earlier in his career, he co-led the development of the RCSB Protein Data Bank, a veritable treasure trove of protein structure information that helped revolutionize the field and paved the way to contemporary AI advances like AlphaFold.

Mura, who holds appointments with the School of Data Science and Department of Biomedical Engineering at UVA, has an extensive background in structural and computational biology, including biochemical and crystallographic studies of RNA-based systems and molecular biophysics of DNA. He views biological systems through the lens of molecular evolution and explores the intersection of these areas with data science.

You can read the full article -; titled "Deep Generative Models of Protein Structure Uncover Distant Relationships Across a Continuous Fold Space" -; on the Nature Communications website.

In a recently published article in Nature Communications, a team of researchers from the University of Virginia -; including Phil Bourne, dean of the School of Data Science, Cam Mura, a senior scientist with the School, and Eli Draizen, a recent UVA alumnus-; offer an AI-driven approach to explore structural similarities and relationships across the protein universe.

Specifically, the authors report a computational framework that can detect and quantify such protein relationships at scale (across myriad proteins), in a novel, flexible, and nuanced manner that combines deep learning-based approaches with a new conceptual model, known as the Urfold, that allows for two proteins to exhibit architectural similarity despite having differing topologies or "folds."

The publication is the culmination of years of work by the Bourne Lab to develop this AI-driven framework, called DeepUrfold, to enable the Urfold theory of structure relationships to be explored systematically and at scale.

Bourne, founding dean of the School of Data Science, is world renowned in the scientific community for his research, including structural bioinformatics and computational biology more broadly. Earlier in his career, he co-led the development of the RCSB Protein Data Bank, a veritable treasure trove of protein structure information that helped revolutionize the field and paved the way to contemporary AI advances like AlphaFold.

Mura, who holds appointments with the School of Data Science and Department of Biomedical Engineering at UVA, has an extensive background in structural and computational biology, including biochemical and crystallographic studies of RNA-based systems and molecular biophysics of DNA. He views biological systems through the lens of molecular evolution and explores the intersection of these areas with data science.

Source:

University of Virginia School of Data Science

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