A Survey of Deep Learning Methods in Protein Bioinformatics and its Impact on Protein Design

PhD Qualifying Examination


Title: "A Survey of Deep Learning Methods in Protein Bioinformatics and its 
Impact on Protein Design"

by

Mr. Weihang DAI


Abstract:

Proteins are sequences of amino acids that serve as the basic building blocks 
of living organisms. Despite rapidly growing databases documenting structural 
and functional information for various protein sequences, our understanding of 
proteins remains limited because of the large possible sequence space and the 
complex inter- and intra-molecular forces. Deep learning, which is 
characterized by its ability to learn relevant features directly from large 
datasets, has demonstrated remarkable performance in fields such as computer 
vision and natural language processing. It has also been increasingly applied 
in recent years to the data-rich domain of protein sequences with great 
success, most notably with Alphafold2's breakout performance in the protein 
structure prediction. The performance improvements achieved by deep learning 
unlocks new possibilities in the field of protein bioinformatics, including 
protein design, one of the most difficult but useful tasks. In this paper, we 
broadly categorize problems in protein bioinformatics into three main 
categories: 1) structural prediction, 2) functional prediction, and 3) protein 
design, and review the progress achieved from using deep learning methodologies 
in each of them. We expand on the main challenges of the protein design problem 
and highlight how advances in structural and functional prediction have 
directly contributed to design tasks. Finally, we conclude by identifying 
important topics and future research directions.


Date:			Wednesday, 10 November 2021

Time:                  	9:30am - 11:30am

Zoom meeting:
https://hkust.zoom.us/j/91556711752?pwd=bnJJb1FhWXI2eDNPR1NBaXBXV0F1QT09

Committee Members:	Prof. Tim Cheng (Supervisor)
 			Dr. Xiaomeng Li (Supervisor)
 			Dr. Yangqiu Song (Chairperson)
 			Prof. Weichuan YU


**** ALL are Welcome ****