Bozitao Zhong

Research Interest

  • Computational Structural Biology: Protein design algorithms, Molecular dynamics, Quantum chemistry


Google Scholar ORCID
  1. B. Zhong et al., ParaFold: Paralleling AlphaFold for Large-Scale Predictions. HPCAsia 2022 Workshop, (2022)
  2. C. Shi, C. Wang, J. Lu, B. Zhong, J. Tang, Protein Sequence and Structure Co-Design with Equivariant Translation, ICLR 2023, (2023)
  3. Y. Zhang, H. Cai, C. Shi, B. Zhong, J. Tang, E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking, ICLR 2023, (2023)
  4. B. Zhong, G. Song, H.-F. Chen, Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site, International Journal of Molecular Sciences. 23, 11285 (2022)
  5. F. Huang et al., Catalytic properties and biological function of a PIWI-RE nuclease from Pseudomonas stutzeri, Bioresour. Bioprocess. 9, 57 (2022)
  6. G. Song, B. Zhong, B. Zhang, A. U. Rehman, H.-F. Chen, J. Chem. Inf. Model. 63, 1602–1614 (2023)
  7. Y. Zhan, Z. Zhang, B. Zhong, S. Misra, J. Tang, DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing (2023)
  8. J. Lu, B. Zhong, J. Tang, Score-based Enhanced Sampling for Protein Molecular Dynamics (2023)
  9. A. U. Rehman et al., Phys. Chem. Chem. Phys. 23, 12204–12215 (2021)


  • Shanghai Jiao Tong University, Shanghai, China, 2020/09-Present
    • B.S. in Computer Science
  • Shanghai Jiao Tong University, Shanghai, China, 2016/09-2020/07
    • B.S. in Bioinformatics
    • Advisor: Prof. Haifeng Chen
  • University of Zurich, Zurich, Switzerland, 2019/09-2020/01
    • Exchange Student

Research Experience

  • Analysis, Assembly and Design of Protein Structural Components
    • PI: Haifeng Chen
  • Semi-Rational Directed Evolution to Improve SpCas9 Fidelity on Specific Genes
    • PI: Gang Ma, Lin He
    • Project Detail & Our Team
    • BioX Institutes, Shanghai Jiao Tong University, 2020 iGEM competition project
    • Build dCas9 activation and inhibition specificity sensor circuit
    • Conduct mutagenesis by error-prone PCR and screening by flow cytometer
    • Perform molecular dynamics simulation of dCas9 on and off-target structure
    • Extract protein features related to its function and find key residues related to the features
    • Use site specific mutagenesis and accelerate directed evolution via semi-rational evolution
  • Precise Force Field ff03PTM for Post-Translational Modified Protein
    • PI: Haifeng Chen
    • Department of Bioinformatics & Biostatistics, Shanghai Jiao Tong University
    • Calculated the potential energy surface of PTM residues
    • Used Correlation Map method to add adjustments parameters
    • Comparatively tested the force field before and after adding CMAP
    • Compared the Cα chemical shift RMSD between experiment and simulation
    • The project was included in 6th ChunTsung Projects (2 in school of life science)
  • CRISPR Off-Target Detection System
  • Test and Evaluation of ff03CMAP force field on Post-Translational Modified Proteins
    • PI: Haifeng Chen
  • Palette - A Universal Multifactorial Visualized Detection System
    • PI: Gang Ma, Lin He
    • Detail
    • BioX Institutes, Shanghai Jiao Tong University, 2017 iGEM competition project
    • Team leader, responsible for project design and team management
    • Used small transcription activating RNA (STAR) to control multifactorial sensory system
    • Designed a new pair of STAR antisense and target and integrated them with the old pair into bacteria
    • Constructed and expressed chromoproteins in E. coli
  • QM/MM calculation of potential-energy curve of target enzyme catalytic reaction and enzyme design adapted to the novel 4+4 cycloaddition reaction
    • Detail
    • Course Project, Instructor: Yilei Zhao
    • Shanghai Jiao Tong University, Computational Biochemistry Course Project
    • Used Gaussian 09 to calculate potential energy curve of enzymatic reaction
    • Compared the effects of different intermediates on the product
    • Constructed structural model of protein’s single amino acid mutant by Swiss-Model
    • Used QM/MM simulation to prove the possibility of the new 4+4 cycloaddition reaction
  • Combinatorial cell surface display system in Escherichia coli for noninvasive colorectal cancer detection
  • Developing Novel Algorithm for Mapping microRNA Targets
    • PI: Ilya Ioshikhes, William Klement
  • Disulfiram Ejection Zinc Mechanism for Nonstructural Protein 5A
    • PI: Haifeng Chen

Honors and Awards

  • Silver Model, iGEM 2020
  • ChunTsung Scholar, 2020
    • Honors excellent undergraduates who completed high-level research projects
  • Gold Medal, Nominated for Best New Application Project, iGEM, 2019
    • As team advisor of SJTU-BioX-Shanghai
  • Ivy Specialty Scholarship, SJTU, 2019
    • Honors student with specialty (scientific competitions), 1 of 16 in university
  • Gold Medal, Nominated for Best Therapeutics Project, iGEM, 2018
    • As team member of SJTU-BioX-Shanghai
  • Hongyi Excellent Scholarship, SJTU, 2018
    • Honors undergraduates did well in scientific research, 1 of 10 in university
  • Gold Medal, iGEM, 2017
    • As team leader of SJTU-BioX-Shanghai
  • A-class Academic Excellent Scholarship, SJTU, 2017
    • Honors top 15% students

Leadership & Activities

  • iGEM Judge, 2021
  • Executive Committee, Conference of China iGEMer Community (CCiC), 2019-2020
  • Mentor, Fudan-TSI iGEM team, 2019
  • Vice Chairman, Student Union of School of Life Sciences and Biotechnology, 2018
  • Group Leader, Editor and Reporter, Yiyou New Media Agency, 2018