公海彩船: 课题组长
姓名:
白芳助理教授 研究员 博士生导师, PhD, 助理教授
职务:
所在院所:
公海彩船、免疫化学研究所
荣誉称号:
教育经历:
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2004/09—2009/07,大连理工大学,双学士
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2009/09—2014/05,上海药物研究所/大连理工大学联合培养,博士
博士后及工作经历:
- 2014/08—2019/05,美国莱斯大学,博士后
- 2019/05—2019/09,美国德克萨斯大学休斯敦健康科学医学中心,助理教授
- 2019/10—至今,上海科技大学,公海彩船,助理教授(TENURE-TRACK)
公海彩船: 课题组简介
研究内容:
本课题组研究方向主要通过结合计算机辅助药物设计、理论生物物理、分子生物学与细胞生物学等方法探索与设计药物设计新方法。 特别侧重于以下方向: 1.结合人工智能算法,发展新型药物设计方法:诸如药物靶标预测方法、成药性位点预测方法,药物分子设计与评价方法、蛋白质-蛋白质互作调控分子,特别是新分子实体(如分子胶水和靶标嵌合体等降解剂分子)的设计方法、蛋白质构象采样和肽分子设计等方法。 2.针对重大疾。绺叻⑿园┲⒂胫卮蟠拘约膊。捎蒙鲜龇椒购蜓≈瘟平橹实纳杓蒲芯。
课题组网站:
https://bailab.siais.shanghaitech.edu.cn/
公海彩船: 研究成果展示
课题组以发展药物设计新方法为主,并致力于新药设计与药物作用靶标发现及机制研究等应用课题,发展了多种药物设计和计算生物学新方法,为药物靶标发现、先导化合物发现和优化等研究开发了多个计算方法与软件;同时,在药物设计、药物作用机制、药物靶标发现等研究中,与中国、美国和以色列的多个团队开展合作,取得了一系列研究成果,先后在Science、PNAS、Nat.Commun.、Chem. Sci.、Nucleic Acids Res.等期刊上发表论文50余篇;担任数十个国际著名期刊编委或审稿人。
公海彩船: 代表性论文(*第一作者,#通讯作者)
- 1. Li, Fenglei*; Hu, Qiaoyu; Zhang, Xianglei; Sun, Renhong; Liu, Zhuanghua; Wu, Sanan; Tian, Siyuan; Ma, Xinyue; Dai, Zhizhuo; Yang, Xiaobao#; Gao, Shenghua#; Bai, Fang#.DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs.NATURE COMMUNICATIONS. 21 Nov 2022. 13(1).
- 2. Li, Jian*; Sun, Jina; Zhang, Xianglei; Zhang, Ruxue; Wang, Qian; Wang, Lin; Zhang, Leike; Xie, Xiong; Li, Chunpu; Zhou, Yu; Wang, Jiang; Xiao, Gengfu#; Bai, Fang#; Liu, Hong#.Synthesis of maleimide-braced peptide macrocycles and their potential anti-SARS-CoV-2 mechanisms.CHEMICAL COMMUNICATIONS. 01 Dec 2022.
- 3. Wang, Qian#*; Wang, Lin; Zhang, Yumin; Zhang, XiangLei; Zhang, Leike; Shang, Weijuan#; Bai, Fang#.Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications.JOURNAL OF MEDICINAL CHEMISTRY. 24 Feb 2022. 65(4).
- 4. Li, Shiwei*; Wu, Sanan; Wang, Lin; Li, Fenglei; Jiang, Hualiang; Bai, Fang#.Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms.CURRENT OPINION IN STRUCTURAL BIOLOGY. Apr 2022. 73.
- 5. Karmi, Ola*; Marjault, Henri-Baptiste; Bai, Fang; Roy, Susmita; Sohn, Yang-Sung; Yahana, Merav Darash; Morcos, Faruck; Ioannidis, Konstantinos; Nahmias, Yaakov; Jennings, Patricia A.; Mittler, Ron; Onuchic, Jose N.#; Nechushtai, Rachel#.A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 15 Feb 2022. 119(7).
- 6. Han, Qi-lei*; Zhang, Xiang-lei; Ren, Peng-xuan; Mei, Liang-he; Lin, Wei-hong; Wang, Lin; Cao, Yu; Li, Kai#; Bai, Fang#.Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma.ACTA PHARMACOLOGICA SINICA. Oct 2022.
- 7. Ren, Peng-xuan*; Shang, Wei-juan*; Yin, Wan-chao*; Ge, Huan*; Wang, Lin*; Zhang, Xiang-lei; Li, Bing-qian; Li, Hong-lin; Xu, Ye-chun; Xu, Eric H.; Jiang, Hua-liang; Zhu, Li-li#; Zhang, Lei-ke#; Bai, Fang#.A multi-targeting drug design strategy for identifying potent anti-SARS-CoV-2 inhibitors.ACTA PHARMACOLOGICA SINICA. Feb 2022.
- 8. Wang, Lin*; Wu, Yan*; Yao, Sheng*; Ge, Huan*; Zhu, Ya; Chen, Kun; Chen, Wen-zhang; Zhang, Yi; Zhu, Wei; Wang, Hong-yang; Guo, Yu; Ma, Pei-xiang; Ren, Peng-xuan; Zhang, Xiang-lei; Li, Hui-qiong; Ali, Mohammad A.; Xu, Wen-qing; Jiang, Hua-liang; Zhang, Lei-ke#; Zhu, Li-li#; Ye, Yang#; Shang, Wei-juan#; Bai, Fang#.Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein.ACTA PHARMACOLOGICA SINICA. Apr 2022.
- 9. Wang, Lin*; Li, Feng-lei; Ma, Xin-yue; Cang, Yong; Bai, Fang#.PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method.JOURNAL OF CHEMICAL INFORMATION AND MODELING. 01 Nov 2022.
- 10. Bai, Fang*; Liu, Kangdong*; Li, Huiliang*; Wang, Jiawei; Zhu, Junsheng; Hao, Pei; Zhu, Lili; Zhang, Shoude; Shan, Lei; Ma, Weiya; Bode, Ann M.; Zhang, Weidong#; Li, Honglin#; Dong, Zigang#.Veratramine modulates AP-1-dependent gene transcription by directly binding to programmable DNA.NUCLEIC ACIDS RESEARCH. 2018. 46(2):546-557.
- 11. Iosub-Amir, Anat*; Bai, Fang*; Sohn, Yang-Sung; Song, Luhua; Tamir, Sagi; Marjault, Henri-Baptiste; Mayer, Guy; Karmi, Ola; Jennings, Patricia A.; Mittler, Ron; Onuchic, Jose N.#; Friedler, Assaf#; Nechushtai, Rachel#.The anti-apoptotic proteins NAF-1 and iASPP interact to drive apoptosis in cancer cells.CHEMICAL SCIENCE. 2019. 10(3):665-673.
- 12. Bai, Fang*; Pi, Xiaoping*; Li, Ping; Zhou, Pingzheng; Yang, Huaiyu; Wang, Xicheng; Li, Min; Gao, Zhaobing#; Jiang, Hualiang#.A Statistical Thermodynamic Model for Ligands Interacting With Ion Channels: Theoretical Model and Experimental Validation of the KCNQ2 Channel.FRONTIERS IN PHARMACOLOGY. 2018. 9.
- 13. Bai, Fang*; Morcos, Faruck; Cheng, Ryan R.; Jiang, Hualiang#; Onuchic, Jose N.#.Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2016. 113(50):8051-8058.
- 14. Bai, Fang*; Morcos, Faruck*; Sohn, Yang-Sung; Darash-Yahana, Merav; Rezende, Celso O.; Lipper, Colin H.; Paddock, Mark L.; Song, Luhua; Luo, Yuting; Holt, Sarah H.; Tamir, Sagi; Theodorakis, Emmanuel A.; Jennings, Patricia A.#; Onuchic, Jose N.#; Mittler, Ron#; Nechushtai, Rachel#.The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2015. 112(12):3698-3703.
- 15. Bai, Fang*; Liao, Sha*; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin#.An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy.JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2015. 55(4):833-847.
- 16. Bai, Fang*; Xu, Yechun; Chen, Jing; Liu, Qiufeng; Gu, Junfeng; Wang, Xicheng; Ma, Jianpeng; Li, Honglin#; Onuchic, Jose N.#; Jiang, Hualiang#.Free energy landscape for the binding process of Huperzine A to acetylcholinesterase.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013. 110(11):4273-4278.
- 17. Bai, Fang*; Liu, Hongyan*; Tong, Linjiang; Zhou, Wei; Liu, Li; Zhao, Zhenjiang; Liu, Xiaofeng; Jiang, Hualiang; Wang, Xicheng#; Xie, Hua#; Li, Honglin#.Discovery of novel selective inhibitors for EGFR-T790M/L858R.BIOORGANIC & MEDICINAL CHEMISTRY LETTERS. 2012. 22(3):1365-1370.
- 18. Bai, Fang*; Liu, Xiaofeng; Li, Jiabo; Zhang, Haoyun; Jiang, Hualiang; Wang, Xicheng#; Li, Honglin#.Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods.BMC BIOINFORMATICS. 2010. 11.
- 19. Jin, Zhenming*; Du, Xiaoyu*; Xu, Yechun*; Deng, Yongqiang*; Liu, Meiqin*; Zhao, Yao; Zhang, Bing; Li, Xiaofeng; Zhang, Leike; Peng, Chao; Duan, Yinkai; Yu, Jing; Wang, Lin; Yang, Kailin; Liu, Fengjiang; Jiang, Rendi; Yang, Xinglou; You, Tian; Liu, Xiaoce; Yang, Xiuna; Bai, Fang; Liu, Hong; Liu, Xiang; Guddat, Luke W.; Xu, Wenqing; Xiao, Gengfu; Qin, Chengfeng; Shi, Zhengli; Jiang, Hualiang#; Rao, Zihe#; Yang, Haitao#.Structure of M-pro from SARS-CoV-2 and discovery of its inhibitors.NATURE. 09 Apr 2020. 582(7811):289–293.
- 20. Lipper, Colin H.*; Stofleth, Jason T.*; Bai, Fang; Sohn, Yang-Sung; Roy, Susmita; Mittler, Ron; Nechushtai, Rachel; Onuchic, Jose N.#; Jennings, Patricia A.#.Redox-dependent gating of VDAC by mitoNEET.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019. 116(40):19924-19929.
- 21. Dai, Wenhao*; Zhang, Bing*; Jiang, Xia-Ming*; Su, Haixia*; Li, Jian; Zhao, Yao; Xie, Xiong; Jin, Zhenming; Peng, Jingjing; Liu, Fengjiang; Li, Chunpu; Li, You; Bai, Fang; Wang, Haofeng; Cheng, Xi; Cen, Xiaobo; Hu, Shulei; Yang, Xiuna; Wang, Jiang; Liu, Xiang; Xiao, Gengfu; Jiang, Hualiang; Rao, Zihe; Zhang, Lei-Ke#; Xu, Yechun#; Yang, Haitao#; Liu, Hong#.Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.SCIENCE. 19 Jun 2020. 368(6497):1331-1335.
- 22. Wang, Haofeng*; Xiao, Yunjie; Chen, Xia; Zhang, Mengwen; Sun, Guangxin; Wang, Feng; Wang, Lin; Zhang, Hanxiao; Zhang, Xiaoyu; Yang, Xin; Li, Wenling; Wei, Yi; Yao, Deqiang; Zhang, Bing; Li, Jun; Cui, Wen; Wang, Fenghua; Chen, Cheng; Shen, Wei; Su, Dan; Bai, Fang; Huang, Jinhai; Ye, Sheng; Zhang, Lei; Ji, Xiaoyun; Wang, Wei; Wang, Zefang; Hochstrasser, Mark; Yang, Haitao.Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue.NATURE COMMUNICATIONS. 25 Mar 2022. 13(1):1608.
- 23. Zhou, Zhongneng*; Chen, Zijing; Kang, Xiu-Wen; Zhou, Yalin; Wang, Bingyao; Tang, Siwei; Zou, Shuhua; Zhang, Yifei; Hu, Qiaoyu; Bai, Fang; Ding, Bei#; Zhong, Dongping#.The nature of proton-coupled electron transfer in a blue light using flavin domain.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 28 Jun 2022. 119(26).
- 24. Bai, Fang#*; Jiang, Hualiang.Computationally Elucidating the Binding Kinetics for Different AChE Inhibitors to Access the Rationale for Improving the Drug Efficacy.JOURNAL OF PHYSICAL CHEMISTRY B. Sep 2022.
- 25. Liu, Haixia*; Mi, Qianglong; Ding, Xinyu; Lin, Chencen; Liu, Linyi; Ren, Chaowei; Shen, Shu Ting; Shao, Yu Bao; Chen, Jinju; Zhou, Yongqi; Ji, Liting; Zhang, Heqiao; Bai, Fang#; Yang, Xiaobao#; Yin, Qianqian#; Jiang, Biao#.Discovery and characterization of novel potent BCR-ABL degraders by conjugating allosteric inhibitor.EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY. 15 Dec 2022. 244.
- 26. Tan, Zheqiong*; Xiao, Lanbo*; Tang, Min*; Bai, Fang; Li, Jiangjiang; Li, Liling; Shi, Feng; Li, Namei; Li, Yueshuo; Du, Qianqian; Lu, Jingchen; Weng, Xinxian; Yi, Wei; Zhang, Hanwen; Fan, Jia; Zhou, Jian; Gao, Qiang; Onuchic, Jose N.; Bode, Ann M.; Luo, Xiangjian#; Cao, Ya#.Targeting CPT1A-mediated fatty acid oxidation sensitizes nasopharyngeal carcinoma to radiation therapy.THERANOSTICS. 2018. 8(9):2329-2347.
- 27. Yim, Kendrick H.*; Prince, Thomas L.; Qu, Shiwei; Bai, Fang; Jennings, Patricia A.; Onuchic, Jose N.; Theodorakis, Emmanuel A.*; Neckers, Leonard#*.Gambogic acid identifies an isoform-specific druggable pocket in the middle domain of Hsp90 beta.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2016. 113(33):4801-4809.
- 28. Darash-Yahana, Merav*; Pozniak, Yair*; Lu, Mingyang*; Sohn, Yang-Sung; Karmi, Ola; Tamir, Sagi; Bai, Fang; Song, Luhua; Jennings, Patricia A.; Pikarsky, Eli; Geiger, Tamar; Onuchic, Jose N.#; Mittler, Ron#; Nechushtai, Rachel#.Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2016. 113(39):10890-10895.
- 29. Wang, Chong*; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Gao, Xiang; Zhou, X. Edward; Melcher, Karsten; Zhang, Chenghai; Bai, Fang; Yang, Huaiyu; Yang, Linlin; Jiang, Hualiang; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C.#; Xu, H. Eric#.Structural Basis for Molecular Recognition at Serotonin Receptors.SCIENCE. 2013. 340(6132):610-614.
公海彩船: 项目
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1. 基于分子片段的蛋白质-蛋白质作用调控剂的设计方法,上海市科委,项目负责人
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2. 抗新型冠状病毒肺炎应急药物的研发,上海市科委,课题负责人
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3. 植物隐花色素蛋白机器光反应的分子动态机制研究,科技部 国家重点研发计划,项目骨干
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4. KRAS突变型分子调控机制的研究与药物设计,国家自然科学基金委,项目负责人
公海彩船: 课题组成员及合影
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姓名:张向磊
身份:博士后
在组时间:2020/07-至今
邮箱:zhangxl6@shanghaitech.edu.cn
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姓名:胡乔宇
身份:博士后
在组时间:2020.10-至今
邮箱:
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姓名:任鹏璇
身份:硕士研究生
在组时间:2019/10-至今
邮箱:renpx@@shanghaitech.edu.cn
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姓名:王林
身份:硕士研究生
在组时间:2019/10-至今
邮箱:wanglin3@@shanghaitech.edu.cn
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姓名:熊若凡
身份:硕士研究生
在组时间:2020/1-至今
邮箱:xiongrf@@shanghaitech.edu.cn
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姓名:吴洒男
身份:硕士研究生
在组时间:2021.1-至今
邮箱:
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姓名:李世伟
身份:硕士研究生
在组时间:2021.1-至今
邮箱:
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姓名:张学远
身份:硕士研究生
在组时间:2021.1-至今
邮箱:
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姓名:刘露
身份:硕士研究生
在组时间:2021.1-至今
邮箱:
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姓名:严帅
身份:本科生
在组时间:2020.1-至今
邮箱:
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姓名:吴汶津
身份:本科生
在组时间:2020.2-至今
邮箱:
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姓名:李冰倩
身份:访问学生
在组时间:2020.7-2020.12
邮箱:
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姓名:李风雷
身份:访问学生
在组时间:2020.11-至今
邮箱:
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