| RNA-specific force field optimization with CMAP and reweighting J Chen, H Liu, X Cui, Z Li, HF Chen Journal of Chemical Information and Modeling 62 (2), 372-385, 2022 | 19 | 2022 |
| Base-specific RNA force field improving the dynamics conformation of nucleotide Z Li, J Mu, J Chen, HF Chen International Journal of Biological Macromolecules 222, 680-690, 2022 | 11 | 2022 |
| Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling J Zhu, Z Li, H Tong, Z Lu, N Zhang, T Wei, HF Chen Briefings in Bioinformatics 25 (1), bbad429, 2024 | 9 | 2024 |
| Research and evaluation of the allosteric protein-specific force field based on a pre-training deep learning model X Ji, X Cui, Z Li, T Choi, Y Wang, W Xiao, Y Zhao, J Zha, J Zhang, ... Journal of Chemical Information and Modeling 63 (8), 2456-2468, 2023 | 6 | 2023 |
| Sequence-based machine learning method for predicting the effects of phosphorylation on protein-protein interactions X Hong, J Lv, Z Li, Y Xiong, J Zhang, HF Chen International Journal of Biological Macromolecules 243, 125233, 2023 | 4 | 2023 |
| Graphormer supervised de novo protein design method and function validation J Mu, Z Li, B Zhang, Q Zhang, J Iqbal, A Wadood, T Wei, Y Feng, HF Chen Briefings in Bioinformatics 25 (3), bbae135, 2024 | 3 | 2024 |
| De novo protein sequence design based on deep learning and validation on CalB Hydrolase J Mu, ZX Li, B Zhang, Q Zhang, J Iqbal, A Wadood, T Wei, Y Feng, H Chen bioRxiv, 2023.08. 01.551444, 2023 | 3 | 2023 |
| Precise Generation of Conformational Ensembles for Intrinsically Disordered Proteins via Fine-tuned Diffusion Models J Zhu, Z Li, Z Zheng, B Zhang, B Zhong, J Bai, X Hong, T Wang, T Wei, ... bioRxiv, 2024.05. 05.592611, 2024 | 2 | 2024 |
| Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields T Choi, Z Li, G Song, HF Chen Journal of Chemical Theory and Computation 20 (6), 2676-2688, 2024 | 2 | 2024 |
| Excited–Ground-State Transition of the RNA Strand Slippage Mechanism Captured by the Base-Specific Force Field Z Li, G Song, J Zhu, J Mu, Y Sun, X Hong, T Choi, X Cui, HF Chen Journal of Chemical Theory and Computation 20 (14), 6082-6097, 2024 | | 2024 |
| Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities H Shadman, JD Ziebarth, CE Gallops, R Luo, Z Li, HF Chen, Y Wang Biophysical Journal 123 (10), 1253-1263, 2024 | | 2024 |
| Scaffold-Lab: Critical Evaluation and Ranking of Protein Backbone Generation Methods in A Unified Framework Z Zheng, B Zhang, B Zhong, K Liu, Z Li, J Zhu, J Yu, T Wei, HF Chen bioRxiv, 2024.02. 10.579743, 2024 | | 2024 |
| Synthesis and degradation of the cyclic dinucleotide messenger c‐di‐AMP in the hyperthermophilic archaeon Pyrococcus yayanosii Z Jin, D Song, WW Wang, L Feng, ZX Li, HF Chen, X Xiao, XP Liu Protein Science 32 (12), e4829, 2023 | | 2023 |
