Theoretical Molecular Science Group banner

Publications

Selected papers

A short selected list is shown here. For a complete and current record, please visit the Google Scholar profile.

Google Scholar
  1. Dynamics of the SS Loop Regulates SARM1′ s Catalysis. Jian Yuan Yang, Wei Ming He, Wan Hua Li, Qianwen Wang, Tsz-Fung Wong, Xiaowan Jin, Dongjie Hu, Jingxuan Gao, Yilin Guo, Zhongping Yao, Deqiang Niu, Hon Cheung Lee, Ying-Chih Chiang, Yong Juan Zhao. ACS Chemical Neuroscience, 2026.
  2. A partition function estimator. Ying-Chih Chiang, Frank Otto, Jonathan W. Essex. The Journal of Chemical Physics, 2025.
  3. Structure modeling and virtual screening with HCAR3 to discover potential therapeutic molecules. Yulan Liu, Yunlu Peng, Zhihao Zhao, Yilin Guo, Bin Lin, Ying-Chih Chiang. Pharmaceuticals, 2025.
  4. Toward high-efficiency, low-resource, and explainable neuropeptide prediction with MSKDNP. Peilin Xie, Jiahui Guan, Zhihao Zhao, Yulan Liu, Zhang Cheng, Xuxin He, Xingchen Liu, Yun Tang, Zhenglong Sun, Tzong-Yi Lee, Lantian Yao, Ying-Chih Chiang. Briefings in Bioinformatics, 2025.
  5. dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era. Lantian Yao, Jiahui Guan, Peilin Xie, Chia-Ru Chung, Zhihao Zhao, Danhong Dong, Yilin Guo, Wenyang Zhang, Junyang Deng, Yuxuan Pang, Yulan Liu, Yunlu Peng, Jorng-Tzong Horng, Ying-Chih Chiang, Tzong-Yi Lee. Nucleic Acids Research, 2025.
  6. ConsAMPHemo: A computational framework for predicting hemolysis of antimicrobial peptides based on machine learning approaches. Peilin Xie, Lantian Yao, Jiahui Guan, Chia‐Ru Chung, Zhihao Zhao, Feiyu Long, Zhenglong Sun, Tzong‐Yi Lee, Ying‐Chih Chiang. Protein Science, 2025.
  7. AMPActiPred: A three‐stage framework for predicting antibacterial peptides and activity levels with deep forest. Lantian Yao, Jiahui Guan, Peilin Xie, Chia‐Ru Chung, Junyang Deng, Yixian Huang, Ying‐Chih Chiang, Tzong‐Yi Lee. Protein Science, 2024.
  8. Structural insights into the activation and inhibition of CXC chemokine receptor 3. Haizhan Jiao, Bin Pang, Aijun Liu, Qiang Chen, Qi Pan, Xiankun Wang, Yunong Xu, Ying-Chih Chiang, Ruobing Ren, Hongli Hu. Nature structural & molecular biology, 2024.
  9. On the force field optimisation of beta-lactam cores using the force field Toolkit. Qiyang Wu, Tianyang Huang, Songyan Xia, Frank Otto, Tzong-Yi Lee, Hsien-Da Huang, Ying-Chih Chiang. Journal of Computer-Aided Molecular Design, 2022.
  10. Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism. Yufei Han, Qian Zhuang, Bo Sun, Wenping Lv, Sheng Wang, Qingjie Xiao, Bin Pang, Youli Zhou, Fuxing Wang, Pengliang Chi, Qisheng Wang, Zhen Li, Lizhe Zhu, Fuping Li, Dong Deng, Ying-Chih Chiang, Zhenfei Li, Ruobing Ren. Nature Communications, 2021.
  11. Molecular dynamics simulations of antibiotic ceftaroline at the allosteric site of penicillin‐binding protein 2a (PBP2a). Ying‐Chih Chiang, Mabel TY Wong, Jonathan W. Essex. Israel Journal of Chemistry, 2020.
  12. Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase. Ying-Chih Chiang, Olesya Levsh, Chun Kei Lam, Jing-Ke Weng, Yi Wang. PLoS Computational Biology, 2018.
  13. The exact wavefunction factorization of a vibronic coupling system. Ying-Chih Chiang, Shachar Klaiman, Frank Otto, Lorenz S Cederbaum. The Journal of Chemical Physics, 2014.
  14. Interrelation between the distributions of kinetic energy release and emitted electron energy following the decay of electronic states. Ying-Chih Chiang, Frank Otto, Hans-Dieter Meyer, Lorenz S Cederbaum. Physical Review Letters, 2011.