ParaFold: Paralleling AlphaFold for Large-Scale Predictions. - Bozitao Zhong; Xiaoming Su; Minhua Wen; Sicheng Zuo; Liang Hong; James Lin (HPC Asia Workshops, 2022)

E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking. - Yangtian Zhang; Huiyu Cai; Chence Shi; Bozitao Zhong; Jian Tang 005 (CoRR, 2022)

Protein Sequence and Structure Co-Design with Equivariant Translation. - Chence Shi; Chuanrui Wang; Jiarui Lu; Bozitao Zhong; Jian Tang 005 (ICLR, 2023)

DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing. - Yangtian Zhang; Zuobai Zhang; Bozitao Zhong; Sanchit Misra; Jian Tang 005 (NeurIPS, 2023)

Score-based Enhanced Sampling for Protein Molecular Dynamics. - Jiarui Lu; Bozitao Zhong; Jian Tang 005 (CoRR, 2023)

PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design. - Chuanrui Wang; Bozitao Zhong; Zuobai Zhang; Narendra Chaudhary; Sanchit Misra; Jian Tang 005 (CoRR, 2023)

Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins. - Ge Song; Bozitao Zhong; Bo Zhang; Ashfaq Ur Rehman; Hai-Feng Chen (J. Chem. Inf. Model., 2023)

Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance? - Yang Tan 001; Lirong Zheng 005; Bozitao Zhong; Liang Hong; Bingxin Zhou (BIBM, 2024)

Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling. - Jiarui Lu; Bozitao Zhong; Zuobai Zhang; Jian Tang 005 (ICLR, 2024)

ReactZyme: A Benchmark for Enzyme-Reaction Prediction. - Chenqing Hua; Bozitao Zhong; Sitao Luan; Liang Hong; Guy Wolf; Doina Precup; Shuangjia Zheng (NeurIPS, 2024)

ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention. - Mingchen Li; Yang Tan 001; Xinzhu Ma; Bozitao Zhong; Huiqun Yu; Ziyi Zhou; Wanli Ouyang; Bingxin Zhou; Pan Tan; Liang Hong (NeurIPS, 2024)

Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations. - Jiarui Lu; Zuobai Zhang; Bozitao Zhong; Chence Shi; Jian Tang 005 (CoRR, 2024)

Autoregressive Enzyme Function Prediction with Multi-scale Multi-modality Fusion. - Dingyi Rong; Wenzhuo Zheng; Bozitao Zhong; Zhouhan Lin; Liang Hong; Ning Liu (CoRR, 2024)

Simple, Efficient, and Scalable Structure-Aware Adapter Boosts Protein Language Models. - Yang Tan 001; Mingchen Li; Bingxin Zhou; Bozitao Zhong; Lirong Zheng 005; Pan Tan; Ziyi Zhou; Huiqun Yu; Guisheng Fan; Liang Hong (J. Chem. Inf. Model., 2024)

Personalized Energy Adaptation through Reweighting Learning (PEARL) Force Field for Intrinsically Disordered Proteins. - Xiaoyue Ji; Junjie Zhu; Bozitao Zhong; Zhengxin Li; Taeyoung Choi; Xiaochen Cui; Ting Wei; Hai-Feng Chen (J. Chem. Inf. Model., 2025)

VenusX: Unlocking Fine-Grained Functional Understanding of Proteins. - Yang Tan 001; Wenrui Gou; Bozitao Zhong; Liang Hong; Huiqun Yu; Bingxin Zhou (CoRR, 2025)