郑铮 简介
男 出生年月：1984年5月
学位： 博士 职称： 教授，博士生导师
Email：johnzhengzz@whut.edu.cn
教育经历：
2008-2013, University of Florida, 化学博士，导师：Prof. Kenneth M. Merz Jr.
2003-2007，北京大学，药学学士
研究经历：
2018.9-今，武汉理工大学，化学化工与生命科学学院，教授
2018.2-2018.8，美国QuantumBio公司，研究员
2014.1-2018.2，美国 Michigan State University，化学系，助理研究员
2009.1-2013.12，美国 University of Florida，研究助理，合作导师：Prof. Kenneth M. Merz Jr.
研究领域：
课题组致力于计算化学、化学及生物信息学与机器学习等领域相关的算法研究与开发，以药物设计和蛋白质工程方向的算法开发，理论研究及程序设计为主要工作方向。提出了“活字印刷”分子自由能算法并完成了相关算法的商业转化。
招收研究生方向：物理化学、计算化学、生物及化学信息学等。欢迎对化学、数学与计算机感兴趣的同学加入课题组。
主要科研项目：
1. 国家自然科学基金青年项目，运用贝叶斯场与深度学习算法开发蛋白质体系的多体能量模型，2020-2022，主持
代表性论文：
1. Xue, S.; Liu, H.; Zheng, Z. Application of the Movable Type Free Energy Method to the Caspase-Inhibitor Binding Affinity Study. Int. J. Mol. Sci. 2019, 20, 4850-4868.
2. Pei, J.; Zheng, Z.; Kim, H.; Song, L. F.; Walworth, S.; Merz, M. R.; Merz Jr., K. M. Random Forest Refinement of Pairwise Potentials for Protein–Ligand Decoy Detection. J. Chem. Inf. Model. 2019, 59, 3305-3315.
3. Pei, J.; Zheng, Z.; Merz Jr., K. M. Random Forest Refinement of the KECSA2 Knowledge-based Scoring Function for Protein Decoy Detection. J. Chem. Inf. Model. 2019, 59, 1919-1929.
4. Zheng, Z.; Pei, J.; Bansal, N.; Liu, H.; Song, L. F. Merz Jr., K. M. Generation of Pairwise Potentials Using Multi-Dimensional Data Mining. J. Chem. Theory Comput. 2018, 14, 5045-5067.
5. Bansal, N.; Zheng, Z.; Song, L. F.; Pei, J.; Merz Jr., K. M. The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation. J. Am. Chem. Soc. 2018, 140, 5434–5446.
6. Zhong, H. A.; Santos, E. M.; Vasileiou, C.; Zheng, Z.; Geiger, J. H.; Borhan, B.; Merz Jr., K. M. Free Energy Based Protein Design: Reengineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach. J. Am. Chem. Soc. 2018, 140, 3483–3486.
7. Burns, L.; Faver, J.; Zheng Z.; Marshall, M.; Smith, D.;Vanommeslaeghe, K.; MacKerell, A.; Merz Jr., K. M.; Sherrill, C. D., The BioFragment Database (BFDb): An Open-Data Platform for Computational Chemistry Analysis of Noncovalent Interactions. J. Chem. Phys. 2017, 147, 161727.
8. Zheng, Z.; Bansal, N.; Cerutti, D.; Merz Jr., K. M., On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. J. Comput. Aided Mol. Des. 2016, 31, 47.
9. Bansal, N.; Zheng, Z.; Merz Jr., K. M., Incorporation of Side Chain Flexibility into Protein Binding Pockets using MTflex. Bioorg. Med. Chem. 2016, 24, 4978–4987.
10. Pan, L.; Zheng, Z.; Wang, T.; Merz Jr., K. M., A Free Energy Based Conformational Search Algorithm Using the “Movable Type” Sampling Method. J. Chem. Theory Comput. 2015, 11, 5853.
11. Han D., Wu C., You M., Zhang T., Wan S., Chen T., Qiu L., Zheng Z., Liang H., Tan W. A cascade reaction network mimicking the basic functional steps of adaptive immune response. Nat. Chem. 2015, 7, 835–841.
12. Zheng, Z.; Wang, T.; Li, P.; Merz, K. M. Jr. KECSA-Movable Type Implicit Solvation Model (KMTISM). J. Chem. Theory Comput. 2014, 11, 667-682.
13. Ucisik, M. N.; Zheng Z.; Faver, J. C.; Merz Jr, K. M., Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”. J. Chem. Theory Comput. 2014, 10, 1314.
14. Zheng, Z.; Ucisik, M. N.; Merz Jr, K. M., The Movable Type Method Applied to Protein–Ligand Binding. J. Chem. Theory Comput. 2013, 9, 5526.
15. Zheng, Z.; Merz Jr, K. M., Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions. J. Chem. Inf. Model. 2013, 53, 1073.
16. Faver, J. C.; Zheng, Z.; Merz Jr, K. M., Statistics-based model for basis set superposition error correction in large biomolecules. Phys. Chem. Chem. Phys. 2012, 14, 7795.
17. Faver, J. C.; Zheng, Z.; Merz, K. M., Jr., Model for the fast estimation of basis set superposition error in biomolecular systems. J. Chem. Phys. 2011, 135, 144110.
18. Zheng, Z.; Merz Jr, K. M., Ligand identification scoring algorithm (LISA). J. Chem. Inf. Model. 2011, 51, 1296.
获奖与荣誉:
中国产学研合作创新奖，2019年
Prof. Zheng Zheng
Email: johnzhengzz@whut.edu.cn
Education
2013 Ph.D. University of Florida
2007 B.Sc. Peking University
Position
2018.9 – Current Professor, Wuhan University of Technology, China
2018.2 – 2018.8 Scientist, QuantumBio Inc., USA
2014.1 – 2018.2 Research Associate, Michigan State University, USA
2008.8 – 2013.12 Research Assistant, University of Florida , USA
Advisor: Prof. Kenneth M. Merz, Jr.
Research Interests
Prof. Zheng’s research interest lies in the development of new computational and quantitative evaluation tools and their application to the molecular thermodynamics and computer-aided molecular design problems including structural based molecule design, protein engineering, molecular free energy simulations, virtual drug candidate screening, etc. He has been heavily involved in the invention and development of new computational algorithms, including molecular free energy methods (the "Movable Type" Method), protein/small molecule conformational search methods (MT-CS and MTflex methods), structural-derived energy function methods (GARF, KECSA, LISA energy functions), etc.
Representative Publications
1. Xue, S.; Liu, H.; Zheng, Z. Application of the Movable Type Free Energy Method to the Caspase-Inhibitor Binding Affinity Study. Int. J. Mol. Sci. 2019, 20, 4850-4868.
2. Pei, J.; Zheng, Z.; Kim, H.; Song, L. F.; Walworth, S.; Merz, M. R.; Merz Jr., K. M. Random Forest Refinement of Pairwise Potentials for Protein–Ligand Decoy Detection. J. Chem. Inf. Model. 2019, 59, 3305-3315.
3. Pei, J.; Zheng, Z.; Merz Jr., K. M. Random Forest Refinement of the KECSA2 Knowledge-based Scoring Function for Protein Decoy Detection. J. Chem. Inf. Model. 2019, 59, 1919-1929.
4. Zheng, Z.; Pei, J.; Bansal, N.; Liu, H.; Song, L. F. Merz Jr., K. M. Generation of Pairwise Potentials Using Multi-Dimensional Data Mining. J. Chem. Theory Comput. 2018, 14, 5045-5067.
5. Bansal, N.; Zheng, Z.; Song, L. F.; Pei, J.; Merz Jr., K. M. The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation. J. Am. Chem. Soc. 2018, 140, 5434–5446.
6. Zhong, H. A.; Santos, E. M.; Vasileiou, C.; Zheng, Z.; Geiger, J. H.; Borhan, B.; Merz Jr., K. M. Free Energy Based Protein Design: Reengineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach. J. Am. Chem. Soc. 2018, 140, 3483–3486.
7. Burns, L.; Faver, J.; Zheng Z.; Marshall, M.; Smith, D.;Vanommeslaeghe, K.; MacKerell, A.; Merz Jr., K. M.; Sherrill, C. D., The BioFragment Database (BFDb): An Open-Data Platform for Computational Chemistry Analysis of Noncovalent Interactions. J. Chem. Phys. 2017, 147, 161727.
8. Zheng, Z.; Bansal, N.; Cerutti, D.; Merz Jr., K. M., On the fly estimation of host–guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge. J. Comput. Aided Mol. Des. 2016, 31, 47.
9. Bansal, N.; Zheng, Z.; Merz Jr., K. M., Incorporation of Side Chain Flexibility into Protein Binding Pockets using MTflex. Bioorg. Med. Chem. 2016, 24, 4978–4987.
10. Pan, L.; Zheng, Z.; Wang, T.; Merz Jr., K. M., A Free Energy Based Conformational Search Algorithm Using the “Movable Type” Sampling Method. J. Chem. Theory Comput. 2015, 11, 5853.
11. Han D., Wu C., You M., Zhang T., Wan S., Chen T., Qiu L., Zheng Z., Liang H., Tan W. A cascade reaction network mimicking the basic functional steps of adaptive immune response. Nat. Chem. 2015, 7, 835–841.
12. Zheng, Z.; Wang, T.; Li, P.; Merz, K. M. Jr. KECSA-Movable Type Implicit Solvation Model (KMTISM). J. Chem. Theory Comput. 2014, 11, 667-682.
13. Ucisik, M. N.; Zheng Z.; Faver, J. C.; Merz Jr, K. M., Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”. J. Chem. Theory Comput. 2014, 10, 1314.
14. Zheng, Z.; Ucisik, M. N.; Merz Jr, K. M., The Movable Type Method Applied to Protein–Ligand Binding. J. Chem. Theory Comput. 2013, 9, 5526.
15. Zheng, Z.; Merz Jr, K. M., Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions. J. Chem. Inf. Model. 2013, 53, 1073.
16. Faver, J. C.; Zheng, Z.; Merz Jr, K. M., Statistics-based model for basis set superposition error correction in large biomolecules. Phys. Chem. Chem. Phys. 2012, 14, 7795.
17. Faver, J. C.; Zheng, Z.; Merz, K. M., Jr., Model for the fast estimation of basis set superposition error in biomolecular systems. J. Chem. Phys. 2011, 135, 144110.
18. Zheng, Z.; Merz Jr, K. M., Ligand identification scoring algorithm (LISA). J. Chem. Inf. Model. 2011, 51, 1296.