Molecular Dynamics and Simulation. - Liangzhen Zheng; Amr Alhossary; Chee-Keong Kwoh 001; Yuguang Mu (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modelling Structure Refinement. - Liangzhen Zheng; Haidong Lan; Tao Shen; Jiaxiang Wu 001; Sheng Wang 001; Wei Liu 005; Junzhou Huang (CoRR, 2021)

Contact-Distil: Boosting Low Homologous Protein Contact Map Prediction by Self-Supervised Distillation. - Qin Wang 011; Jiayang Chen; Yuzhe Zhou; Yu Li 006; Liangzhen Zheng; Sheng Wang 001; Zhen Li 026; Shuguang Cui (AAAI, 2022)

Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term. - Liangzhen Zheng; Jintao Meng 001; Kai Jiang; Haidong Lan; Zechen Wang; Mingzhi Lin; Weifeng Li; Hongwei Guo; Yanjie Wei; Yuguang Mu (Briefings Bioinform., 2022)

E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction. - Tao Shen; Zhihang Hu; Zhangzhi Peng; Jiayang Chen; Peng Xiong; Liang Hong; Liangzhen Zheng; Yixuan Wang; Irwin King; Sheng Wang; Siqi Sun; Yu Li 006 (CoRR, 2022)

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function. - Zechen Wang; Liangzhen Zheng; Sheng Wang 001; Mingzhi Lin; Zhihao Wang; Adams Wai-Kin Kong; Yuguang Mu; Yanjie Wei; Weifeng Li (Briefings Bioinform., 2023)

Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design. - Hilbert Yuen In Lam; Robbe Pincket; Hao Han; Xing Er Ong; Zechen Wang; Jamie Hinks; Yanjie Wei; Weifeng Li; Liangzhen Zheng; Yuguang Mu (Nat. Mac. Intell., 2023)

A new paradigm for applying deep learning to protein-ligand interaction prediction. - Zechen Wang; Sheng Wang 001; Yangyang Li; Jingjing Guo; Yanjie Wei; Yuguang Mu; Liangzhen Zheng; Weifeng Li (Briefings Bioinform., 2024)

Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modeling. - Zhihao Wang; Fan Zhou; Zechen Wang; Qiuyue Hu; Yong-Qiang Li; Sheng Wang; Yanjie Wei; Liangzhen Zheng; Weifeng Li; Xiangda Peng (J. Chem. Inf. Model., 2024)

Evaluations of the Perturbation Resistance of the Deep-Learning-Based Ligand Conformation Optimization Algorithm. - Minghui Xin; Zechen Wang; Zhihao Wang; Yuanyuan Qu; Yanmei Yang; Yong-Qiang Li; Ming-Wen Zhao; Liangzhen Zheng; Yuguang Mu; Weifeng Li (J. Chem. Inf. Model., 2025)