The 15th edition of Computing+ Seminar was held on 27 Jun, 2023. Professor Shi-jie Chen from University of Missouri presented his work 'Unveiling the Intricacies of RNA Folding: Exploring Cotranscriptional Folding through Physical Modeling and Metal Ion Binding with Deep Learning'. The seminar was chaired by Dr. Dong Zhang from Zhejiang University. Professor Ruhong Zhou, Professor Liquan Huang and young researchers from Zhejiang University and Shanghai Institute for Advanced Study, Zhejiang University participated in the seminar on site and online.
Emerging biomedical advances, such as precision medicine and synthetic biology, point to RNA as the central information carrier and functional regulator. Researchers are increasingly interested in predicting RNA structure and function from the nucleotide sequence, as well as in computationally designing and discovering molecules for therapeutic applications. Using machine learning and physics-based computational modeling, professor Chen and his group have recently developed new methods to tackle these problems. I will describe two of these new advances.
In the first part of the talk, professor Chen focused on computational modeling, combined with NMR experiments, of viral RNA folding during transcription. He employed HIV-1 TAR as an example to explore the underlying kinetic control mechanism of transcriptional gene regulation. The computationally revealed TAR folding routes could help researchers develop transcriptional folding-targeted drugs more effectively.
Magnesium ions (Mg2+) are vital for RNA structure and cellular functions, yet accurately identifying the ion binding sites remains a challenge. In the second part of the talk, Professor Chen described a machine-learning method that incorporates geometrical and electrostatic features of RNA to predict the Mg2+ ion binding sites for a given RNA. This new approach could be combined with X-ray crystallography structure determination experiments to accurately pinpoint the metal ion binding sites.
The audience showed great interest in Professor Chen's lecture and asked questions during the Q&A session. Professor Chen patiently answered all questions and engaged in an intense discussion with audiences onsite and online. The seminar was a success and continued the tradition of the Computing+ series.
About “Computing+” Seminar
The revolution characterized by intelligent computing has continued to drive the pervasive application of algorithms and computing power to information, life, and physical sciences, accelerating the construction of a joint world of human, physical world, intelligent machine and digital information science.
In this light, Shanghai Institute for Advanced Study, Zhejiang University launched 'Computing+' seminar series, inviting academics to share latest developments and exchange ideas and thoughts to further explore the intersections of computing with life sciences, engineering and social sciences.