Ke Chen

Dr. Ke Chen serves as a Special-Term Associate Research Fellow at the Suzhou Institute for Advanced Research, University of Science and Technology of China. He obtained his Ph.D. in Physics from Nanjing University in 2019, with his research focusing on elucidating intricate interactions within complex biomacromolecular systems and advancing structure prediction/design methodologies for biomacromolecules. As a core member of the AIChemy-RNA2 team, Dr. Chen contributed to securing first place in the RNA structure prediction category at CASP15 (Critical Assessment of protein Structure Prediction) in 2022, the premier global competition in computational structural biology.

Career

2023/04-Current， Suzhou Institute for Advanced Research, USTC, Special-Term Associate Research Fellow

2022/07-2023/03，Shanghai Zhiyu Biotechnology Co., Ltd., Senior Research Fellow

2020/06-2022/06，Shenzhen Bay Labortary, Postdoctoral Fellow

Email

klarkchen@ustc.edu.cn

Research Interests

Development of RNA 3D modeling and design tools

Awards

1st Place, RNA category, CASP15(2022)

Main Publications

1.    Chen, K., Zhou, Y., Wang, S. & Xiong, P. RNA tertiary structure modeling with BRiQ potential in CASP15. Proteins: Structure, Function, and Bioinformatics 91, 1771–1778 (2023).

2.     Chen, K., Litfin, T., Singh, J., Zhan, J. & Zhou, Y. MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. Genomics, Proteomics & Bioinformatics qzae018 (2024) 

3.     Zhang, Y., Lang, M., Jiang, J., Gao, Z., Xu, F., Litfin, T., Chen, K., Singh, J., Huang, X., Song, G., Tian, Y., Zhan, J., Chen, J. & Zhou, Y. Multiple sequence alignment-based RNA language model and its application to structural inference. Nucleic Acids Research gkad1031 (2023). 

4.     Xu, Y., Chen, K., Pan, J., Lei, Y., Zhang, D., Fang, L., Tang, J., Chen, X., Ma, Y., Zheng, Y., Zhang, B., Zhou, Y., Zhan, J. & Xu, W. Repurposing clinically approved drugs for COVID-19 treatment targeting SARS-CoV-2 papain-like protease. International Journal of Biological Macromolecules 188, 137–146 (2021).

5.     Chen, X., Chen, K., Zhang, Z., Wei, P., Zhang, L., Xu, Y., Lun, Q., Ma, Y., Wu, F., Zhang, Y., Wang, Y., Zhao, J., Zhou, Y., Zhan, J. & Xu, W. Investigating Derivatives of Tanshinone IIA Sulfonate Sodium and Chloroxine for Their Inhibition Activities against the SARS-CoV-2 Papain-like Protease. ACS Omega 7, 48416–48426 (2022).

6.     Chen, K., Sheng, Y., Wang, J. & Wang, W. Chirality-Dependent Adsorption between Amphipathic Peptide and POPC Membrane. International Journal of Molecular Sciences 20, 4760 (2019).

7.   Chen, K., Li, W., Wang, J. & Wang, W. Binding of Copper Ions with Octapeptide Region in Prion Protein: Simulations with Charge Transfer Model. J. Phys. Chem. B 123, 5216–5228 (2019).