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Master students from DSI enable the construction of integrated database for enzyme design

Posted by on Thursday, October 27, 2022 in College of Arts and Science, Natural and Life Sciences, Newsletter.

Enzymes are the “magical powders” that have been invented by nature to accelerate chemical reactions from eons ago. They are extremely good but are mostly limited to the biochemical reactions they are created for. As an enzyme designer, Prof. John Yang, a DSI affiliate from the Department of Chemistry and the Department of Chemical and Biomolecular Engineering, nucleates a research program that aims to create designer enzymes for producing biofuels, degrading pollutant, synthesizing drugs, and even treating diseases.

Lying in the core of their approach is data science. “Data-driven modeling transforms the way we design enzyme, but quality enzymology data with well-defined structure-function relationship are in urgent need.” John said. “The fundamental challenges are enzymology data collection, cleaning, and joining. Those are the questions to which data scientists are in the best position to answer.”

Motivated to address these challenges, Lucy Yan, a student of Biostatistics in John’s lab, together with three DSI students, including Li Yuan, Sarah Torrence, and Alvin Chen, developed an integrated structure–function enzymology database, named IntEnzyDB. After two years of effort, they established the database, along with a web-interface designed by Xinchun Ran and Anvita Gollu to allow public access ( The database holds great promise to enable facile statistical modeling and machine learning.

This research was published in the Journal of Chemical Information and Modeling, a flagship journal in the field of computational chemistry. Due to its broad interest, this research work was selected by ACS Editor’s Choice program as “the paper of the day” among ~100 articles published around the same time across the entire portfolio of American Chemical Society Publications (64+ peer-reviewed journals).

“I am grateful for DSI that offers an integrated environment for research and education. Our students, through the immersive experience of participating collaborative projects led by Dr. Spencer-Smith and other colleagues in DSI, have begun making impacts in academia even before stepping into the industries,” said Prof. John Yang. “I want to particularly thank Dr. Jesse Spencer-Smith for numerous inspiring discussions and Dr. Warren Eckstein for his generous help to set up the web interface on ACCRE!”

Link to the research publication:

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