Fall 2021 Electrical Engineering and Computer Science (EECS) Seminar Series

"Protein Structure Prediction by Deep Learning"
Dr. Jinbo Xu, Toyota Technological Institute at Chicago

Faculty Host: Professor Xiaoyi Lu

Abstract:
Accurate description of protein structure and function is a fundamental step towards understanding biological life and highly relevant in the development of therapeutics. Although greatly improved, experimental protein structure determination is still low-throughput and costly, especially for membrane proteins. As such, computational structure prediction is often resorted. Predicting the structure of a protein without detectable homologs in PDB is very challenging and usually needs a large amount of computing power. This talk will present some deep learning methods (deep convolutional residual neural network and Transformers) that have revolutionized protein structure prediction, and show that even with only a personal computer deep learning may predict the structure of a protein much more accurately than ever before.

Speaker Bio:
Dr. Jinbo Xu is a full professor at the Toyota Technological Institute at Chicago, a computer science research and educational institute affiliated with the University of Chicago. Dr. Xu’s research lies in machine learning, optimization and computational biology. He has developed several popular bioinformatics programs such as the CASP-winning RaptorX (http://raptorx.uchicago.edu) for protein structure prediction and IsoRank/HubRank for biological network analysis. The deep learning method invented by him for protein structure prediction has been widely adopted by the community and initiated the revolution of protein structure prediction, due to which he was invited to give a keynote talk at the 2019 3DSIG session of ISMB, the largest bioinformatics conference in the world. Dr. Xu is an Associate Editor of <> and has received many awards, including Alfred P. Sloan Research Fellowship, NSF CAREER award, RECOMB's Test-of-Time award, RECOMB best paper award 2014 and PLoS Computational Biology Research Prize. Dr. Xu is one keynote speaker at the 2021 Future Science Prize week and one invited speaker at the 2022 Nobel Symposium (NS184) at Stockholm, Sweden.