A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. - Zhuo Zhang; Shiwei Sun; Xiaopeng Zhu; Suhua Chang; Xiaofei Liu; Chungong Yu; Dongbo Bu; Runsheng Chen (BMC Bioinform., 2006)

An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. - Chungong Yu; Yu Lin 001; Shiwei Sun; Jinjin Cai; Jingfen Zhang; Dongbo Bu; Zhuo Zhang; Runsheng Chen (J. Bioinform. Comput. Biol., 2007)

A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. - Yu Lin 001; Yantao Qiao; Shiwei Sun; Chungong Yu; Gongjin Dong; Dongbo Bu (RECOMB, 2008)

Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model. - Shiwei Liu; Tian Zhu; Milong Ren; Chungong Yu; Dongbo Bu; Haicang Zhang (NeurIPS, 2023)

Protein Structure Prediction: Challenges, Advances, and the Shift of Research Paradigms. - Bin Huang; Lupeng Kong; Chao Wang; Fusong Ju; Qi Zhang; Jianwei Zhu; Tiansu Gong; Haicang Zhang; Chungong Yu; Wei-Mou Zheng; Dongbo Bu (Genom. Proteom. Bioinform., 2023)

Accurate and efficient protein sequence design through learning concise local environment of residues. - Bin Huang; Tingwen Fan; Kaiyue Wang; Haicang Zhang; Chungong Yu; Shuyu Nie; Yangshuo Qi; Wei-Mou Zheng; Jian Han; Zheng Fan; Shiwei Sun; Sheng Ye; et al. (Bioinform., 2023)

Accurate and robust protein sequence design with CarbonDesign. - Milong Ren; Chungong Yu; Dongbo Bu; Haicang Zhang (Nat. Mac. Intell., 2024)

GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states. - Fan Liu; Han Zhou; Xiaonong Li; Liangliang Zhou; Chungong Yu; Haicang Zhang; Dongbo Bu; Xinmiao Liang (BMC Bioinform., 2024)

A survey on deep learning-based algorithms for the traveling salesman problem. - Jingyan Sui; Shizhe Ding; Xulin Huang; Yue Yu; Ruizhi Liu; Boyang Xia; Zhenxin Ding; Liming Xu; Haicang Zhang; Chungong Yu; Dongbo Bu (Frontiers Comput. Sci., 2025)