Bozitao Zhong
Research Interest
- Computational Structural Biology: Protein design algorithms, Molecular dynamics, Quantum chemistry
Publications
- B. Zhong et al., ParaFold: Paralleling AlphaFold for Large-Scale Predictions. HPCAsia 2022 Workshop, (2022)
- C. Shi, C. Wang, J. Lu, B. Zhong, J. Tang, Protein Sequence and Structure Co-Design with Equivariant Translation, ICLR 2023, (2023)
- Y. Zhang, H. Cai, C. Shi, B. Zhong, J. Tang, E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking, ICLR 2023, (2023)
- 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)
- F. Huang et al., Catalytic properties and biological function of a PIWI-RE nuclease from Pseudomonas stutzeri, Bioresour. Bioprocess. 9, 57 (2022)
- G. Song, B. Zhong, B. Zhang, A. U. Rehman, H.-F. Chen, J. Chem. Inf. Model. 63, 1602–1614 (2023)
- Y. Zhan, Z. Zhang, B. Zhong, S. Misra, J. Tang, DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing (2023)
- J. Lu, B. Zhong, J. Tang, Score-based Enhanced Sampling for Protein Molecular Dynamics (2023)
- A. U. Rehman et al., Phys. Chem. Chem. Phys. 23, 12204–12215 (2021)
Education
- Shanghai Jiao Tong University, Shanghai, China, 2020/09-Present
- 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
Research Experience
- Analysis, Assembly and Design of Protein Structural Components
- 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
- 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
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
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