裴剑锋

2019-08-20 15:17:18 9

 

裴剑锋

 

博士生导师

 

电话:010-62759669
电子信箱:jfpei_at_pku.edu.cn

 

19957月本科毕业于武汉大学生命科学学院;

19987月于中国科学院武汉病毒研究所获得硕士学位;20027月于中国科学院过程工程研究所获得博士学位。

 

担任职务:

北京大学定量生物学中心特聘研究员

 

 

研究方向:

药物设计与人工智能药物研发

 

 

研究兴趣:

基于靶标的药物分子设计、多靶标药物设计,小分子对生物网络调控作用,人工智能药物研发。

 

 

工作经历:

200210月至20068月在北京大学物理化学研究所和理论生物学中心做博士后研究;

200510月至20067月在美国纽约州立大学布法罗分校医学院做访问研究;20069月起在北京大学前沿交叉学科研究院任职。

 

 

代表性文章:

 

1.    Xu, Y.; Wang, S.; Hu, Q.; Gao, S.; Ma, X.; Zhang, W.; Shen, Y.; Chen, F.; Lai, L.*; Pei, J.*,  CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction.  Nucleic acids research 2018, gkx380.

2.    Feng, F.; Lai L.; Pei, J.*, Computational chemical synthesis analysis and pathway design, Frontiers in Chemistry 2018

3.     li, X.; Xu, Y.; Lai L.; Pei, J.*, Prediction of human cytochrome P450 inhibition using a multi-task deep autoencoder neural network . Molecular Pharmaceutics, 2018

4.    Zhang, W.; Pei, J.*; Lai, L.*, Computational multitarget drug design. Journal of chemical information and modeling 2017, 57 (3), 403-412.

5.     Xu, Y.; Pei, J.*; Lai, L.*, Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction. Journal of chemical information and modeling 2017, 57 (11), 2672-2685.

6.    Wang, X.; Shen, Y.; Wang, S.; Li, S.; Zhang, W.; Liu, X.; Lai, L.; Pei, J.*; Li, H.*, PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. Nucleic acids research 2017, gkx374.

7.    Sun, T.; Zhou, B.; Lai, L.; Pei, J.*, Sequence-based prediction of protein protein interaction using a deep-learning algorithm. BMC Bioinformatics 2017, 18 (1), 277.

8.    Gu, S.; Pei, J.*, Innovating Chinese Herbal Medicine: From Traditional Health Practice to Scientific Drug Discovery. Frontiers in pharmacology 2017, 8, 381.

9.    Li, T.; Yin, N.; Liu, H.; Pei, J.*; Lai, L., Novel inhibitors of toxin HipA reduce multidrug tolerant persisters. ACS medicinal chemistry letters 2016, 7 (5), 449-453.

10.   Zhao, L.; Sun, T.; Pei, J.*; Ouyang, Q.*, Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis. Proceedings of the National Academy of Sciences 2015, 112 (30), E4046-E4054.

11.  Xu, Y.; Dai, Z.; Chen, F.; Gao, S.; Pei, J.*; Lai, L.*, Deep learning for drug-induced liver injury. Journal of chemical information and modeling 2015, 55 (10), 2085-2093.

12.  Wang, X.; Chen, H.; Yang, F.; Gong, J.; Li, S.; Pei, J.*; Liu, X.; Jiang, H.; Lai, L.; Li, H.*, i Drug: a web-accessible and interactive drug discovery and design platform. Journal of cheminformatics 2014, 6 (1), 28.

13.  Shang, E.; Yuan, Y.; Chen, X.; Liu, Y.*; Pei, J.*; Lai, L.*, De novo design of multitarget ligands with an iterative fragment-growing strategy. Journal of chemical information and modeling 2014, 54 (4), 1235-1241.

14.  Pei, J.; Yin, N.; Ma, X.; Lai, L., Systems biology brings new dimensions for structure-based drug design. Journal of the American Chemical Society 2014, 136 (33), 11556-11565.

15.  Yuan, Y.; Pei, J.*; Lai, L., Binding site detection and druggability prediction of protein targets for structure-based drug design. Current pharmaceutical design 2013, 19 (12), 2326-2333.

16.  Gu, S.; Yin, N.; Pei, J.*; Lai, L., Understanding molecular mechanisms of traditional Chinese medicine for the treatment of influenza viruses infection by computational approaches. Molecular BioSystems 2013, 9 (11), 2696-2700.

17.  Yuan, Y.; Pei, J.*; Lai, L.*, LigBuilder 2: a practical de novo drug design approach. Journal of chemical information and modeling 2011, 51 (5), 1083-1091.

18.  Ni, S. S.; Yuan, Y. X.; Huang, J.; Mao, X. N.; Lv, M. S.; Zhu, J.; Shen, X.; Pei, J. F*.; Lai, L. H.; Jiang, H. L.; Li, J.*, Discovering Potent Small Molecule Inhibitors of Cyclophilin A Using de Novo Drug Design Approach. Journal of Medicinal Chemistry 2009, 52, (17), 5295-5298.

19.  Ju, X. L*.; Hao, Y. L.; Pei, J. F*.; Ozoe, Y. S., Investigation of structural requirements for inhibitory activity at the rat and housefly picrotoxinin binding sites in ionotropic GABA receptors using DISCOtech and CoMFA. Chemosphere 2007, 69, (6), 864-871.

20   Pei, J. F.; Wang, Q.; Liu, Z. M.; Li, Q. L.; Yang, K.; Lai, L. H., PSI-DOCK: Towards highly efficient and accurate flexible ligand docking. Proteins-Structure Function and Bioinformatics 2006, 62, (4), 934-946.

21.  Pei, J. F.; Chen, H.; Liu, Z. M.; Han, X. F.; Wang, Q.; Shen, B.; Zhou, J. J.; Lai, L. H., Improving the quality of 3D-QSAR by using flexible-ligand receptor models. Journal of Chemical Information and Modeling 2005, 45, (6), 1920-1933.

22.  Pei, J. F.; Wang, Q.; Zhou, J. J.; Lai, L. H., Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation. Proteins-Structure Function and Bioinformatics 2004, 57, (4), 651-664.

 

 

 

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