曹洋 博士， 副教授
cy_scu.AT.yeah.net（为避免垃圾邮件，请把.AT.换成@）
http://cao.labshare.cn
研究兴趣：
1)药物分子设计算法与应用
2)蛋白设计和三维结构预测
3)序列分析与功能预测
主要成果：
1)建立了CYSCORE、CB-Dock、FitDock、LigMate、CIS-RR等一系列分子模拟与设计算法与软件，获广泛使用，先后发现了针对MDM2、HSP70、 AchE、PB等药物靶点的活性化合物。
2)发展蛋白设计算法EvoDesign，成功设计出多个靶向HER2、EGFR等药物靶标的高稳定性、高亲和力、抗聚集的人工多肽、蛋白 。
3)建立AbRSA，AbAlign等抗体分析算法，成功完成新冠抗体R3P1-E4的亲和力优化、肿瘤靶标HMGB1、PrPc、 PD1抗体的人源化设计。
工作经历：
2014-今， 四川大学，生命科学学院，副教授
2011-2014，四川大学，生命科学学院，讲师
教育经历：
2020-2021，美国哈佛大学，生物信息，X. Shirley Liu Lab
2016-2017，美国密歇根大学，生物信息，Yang Zhang Lab
2004-2010，中科院生物物理所，生物信息，博士
2000-2004，西南交通大学，应用物理，学士
主要论著：
1. Y Liu, X Yang, J Gan, S Chen, ZX Xiao, Y Cao*. CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Research. In press, 2022.
2. X, Yang, Y Liu, J Gan, ZX Xiao, Y Cao*. FitDock: protein–ligand docking by template fitting. Briefings in Bioinformatics. doi.org/10.1093/bib/bbac087, 2022
3. Y Liu, J Gan, R Wang, X Yang, Z Xiao, Y Cao*. DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design. Molecules 27 (3), 683, 2022.
4. M Niu , J Xu , Y Liu , Y Li , T He , L Ding , Y He , Y Yi , F Li , R Guo , Y Gao , R Li , L Li , M Fu , Q Hu , Y Luo , C Zhang , K Qin , J Yi , S Yu , J Yang , H Chen , L Wang , Z Li , B Dong , S Qi , L Ouyang , Y Zhang , Y Cao*, ZX Xiao*. FBXL2 counteracts Grp94 to destabilize EGFR and inhibit EGFR-driven NSCLC growth. Nature Communications. 12, 1-15, 2021
5. L Song, D Cohen, Z Ouyang, Y Cao, X Hu, XS Liu*. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nature Methods. 18，627-630, 2021
6. J Nie#, Q Li#, L Zhang#, Y Cao#, Y Zhang, T Li, J Wu, S Liu, M Zhang,C Zhao, H Liu, L Nie, H Qin, M Wang, Q Lu, X Li, J Liu, H Liang, T Jiang, K Duan, X Yang, Y Shen, W Huang and Y Wang. Functional comparison of SARS-CoV-2 with closely related pangolin and bat coronaviruses. Cell Discovery . 6;7(1):21, 2021
7. Y Liu#, H He#, ZX Xiao, A Ji, J Ye, Q Sun*, Y Cao*. A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification. Briefings in Bioinformatics. 22(4):bbaa324, 2021
8. M Grimm, Y Liu, X Yang, C Bu, ZX Xiao, and Y Cao*. LigMate: A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening. Journal of Chemical Information and Modeling. 60(12):6044-6053, 2020
9. J Zhao, Y Cao*, L Zhang*. Exploring the computational methods for protein-ligand binding site prediction. Computational and structural biotechnology. 18,417-426, 2020
10. Z Zhu, Y Fan, Y Liu, T Jiang, Y Cao*, Y Peng*. Prediction of antiviral drugs against African swine fever viruses based on protein–protein interaction analysis. PeerJ, 8, e8855, 2020
11. Y Liu#, M Grimm#, W Dai, M Hou, ZX Xiao, Y Cao*. CB-Dock: a web server for cavity detection-guided protein-ligand blind docking. Acta Pharmacologica Sinica. 41,138-144, 2020 (ESI高被引论文)
12. L Li#, S Chen#, Z Miao#, Y Liu, X Liu, ZX Xiao and Y Cao*. AbRSA: a Robust Tool for Antibody Numbering. Protein Science. 28, 1524-1531, 2019
13. Y Cao, W Dai, Z Miao. Evaluation of Protein-Ligand Docking by Cyscore. Methods in molecular biology 1762, 233-243, 2018
14. B Kong#, Y Cao#, D Wu, L An, F Ran, Y Lin, C Ye, H Wang*, H Hang*. Affinity maturation of an antibody for the UV-induced DNA lesions 6,4 pyrimidine-pyrimidones. Applied Microbiology and Biotechnology. 102(15) 6409-6424, 2018
15. C Li#, Z Wang#, Y Cao#, L Wang, J Ji, Z Chen, T Deng, T Jiang*, G Cheng*, F Qin*. Screening for Novel Small-Molecule Inhibitors Targeting the Assembly of Influenza Virus Polymerase Complex by a Bimolecular Luminescence Complementation-Based Reporter System. J Virol. 91(5): e02282-16, 2017
16. Z Miao* and Y Cao*. Quantifying side-chain conformational variations in protein structure. Scientific Reports. 6: 37024, 2016
17. J Liu#, Z Miao#, L Li, ZX Xiao*, Y Cao*. DRSP: a Structural Database for Single Residue Substitutions in PDB. Progress in Biochemistry and Biophysics. 43(8):810-816, 2016
18. J Guo#, Y Cao#, K Qin, X Zhao, D Wang, Z Li, L Xin,Y Shu, J Zhou*. Limited effect of recombinant human mannose-binding lectin on the infection of novel influenza A (H7N9) virus in vitro. Biochem Biophys Res Commun. 458(1):77-81, 2015
19. Y Cao*, L Li., Improved protein-ligand binding affinity prediction by using a curvature dependent surface area model, Bioinformatics, 30(12):1674-1680, 2014 (ESI高被引论文)
20. L Huang#, Y Cao#, J Zhou, K Qin, W Zhu, Y Zhu, L Yang, D Wang, H Wei*, Y Shu*., A conformational restriction in influenza A virus neuraminidase binding site by R152 caused the combinational effect of I222T with H274Y on oseltamivir resistance. Antimicrob Agents Chemother. 58(3), 1639-1645, 2014
21. Y Cao#, L Song#, Z Miao, Y Hu, L Tian, T Jiang*., Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation, Bioinformatics, 27(6), 785-790, 2011
22. Y Cao#, X Koh#, L Dong#, X Du, A Wu, X Ding, H Deng, Y Shu*, J Chen*, T Jiang*., Rapid Estimation of Binding Activity of Influenza Virus Hemagglutinin to Human and Avian Receptors, PLoS One, 6(4):e18664, 2011
