2023 has been an extraordinary year, marked by significant achievements and numerous accolades for our group members. Qingyang, Jiaxuan, Zefeng, Ruihan, Kai, and Lingfeng have each secured various scholarships, and Song distinguished himself by earning the President's Scholarship from Peking University (PKU). Zhongjie and Nanhao have both been awarded highly competitive postdoctoral fellowships. And Chen was granted tenure. Congratulations to everyone!
Congratulations to Jiaxuan on the successful publication of her new paper online! Since March 2019, Jiaxuan has diligently pursued the investigation of whether a deep learning-based approach can effectively generate de novo predictions for multiple state structures from a protein sequence. The outcomes of this research were very promising, leading Jiaxuan to devise a new protocol for modeling the alternative conformations from a given protein structure. Despite encountering a long and intricate review process across various journals, the paper has now been published online in the Journal of Chemical Information and Modeling (JCIM). Special recognition goes to Lei and Zefeng for their invaluable contributions to the paper too.
Chen was invited to give a talk at the Molecular Modelling Conference 2023 (MM2023). This Australasia's premier molecular modelling conference was held at the main campus of the University of Wollongong, Australia, 7-10 Dec 2023, organised by the Association of Molecular Modellers of Australasia (AMMA). Chen talked about our recent series of work on Ca2+ channels.
Our collaborative efforts with Prof. Sai Li at Tsinghua University to model and simulate SARS-CoV-2 have been published in Quantitative Biology. Undertaking the challenging task of intricately modeling SARS-CoV-2, we have gained extensive experience in dealing with such complex systems, drawing from our own investigations as well as the research papers of other teams. Dali and Jiaxuan dedicated significant time and effort to modeling the virion structure as accurately as possible, leading to the discovery of interesting dynamics of viral proteins and lipids during coarse-grained Martini simulations. Additionally, we were fortunate to utilize China's E-scale Tianhe-3 supercomputer, conducting all-atom simulations on the massive system comprising 274,193,494 atoms.
We have been collaborating with Prof. Yan's team to study the structures and functions of Cav1.2, and Lingfeng has done a wonderful job in identifying the functional state of a novel Cav1.2 structure by using all-atom MD simulations. Our collaborative paper has been published in Cell, and we anticipate sharing more interesting stories in the future.
Chen was invited to give a talk at the "The 10th Federation of the Asian and Oceanian Physiological Societies Congress" at Daegu, Korea. Our recent work on calcium ion channels was presented at the "Computational Physiology of Ion Channels" symposium on 1 Nov 2023.
Some of us attended the 12th National Conference on Bioinformatics and Systems Biology of China at Tsingtao, 27-30 Oct 2023.
Congrats to Lingfeng! He has passed his qualifying exam, and will continue to pursue his PhD in the group.
Chen was invited to visit the Max Planck Institute for Multidisciplinary Sciences at Göttingen, which was called the Max Planck Institute for Biophysical Chemistry previously. The academic meeting was to celebrate the 20th anniversary of the Department of Theoretical and Computational Biophysics. It was a wonderful event that stimulated lots of old memories and new ideas.
The TRPV paper is online in the Journal of General Physiology! Congrats to Chunhong and Lingfeng! They used our multisite calcium model to simulate the ion permeation and binding patterns in TRPV1 and TRPV6, uncovering distinct features for these two channels. Chunghong had to work on weekends to finish this project, as she left the group a year ago and worked in a company. Lingfeng made a substantial contribution to conducting all the PMF calculations for the revision. Great teamwork! Special thanks go to Dr. Ives and Prof. Zachariae at the University of Dundee for their insightful discussions and invaluable advice.
