戚逸飞

药物化学,副研究员,硕士生导师

发布时间:2021-10-20浏览次数:5042

姓      名

戚逸飞

性      别

 男

职      称

副研究员

学      历

 博士

电      话


传      真


电子邮件

 yfqi@fudan.edu.cn

个人主页

http://protein.org.cn/gs

通讯地址



教育经历

2002—2006北京大学物理学院  理学学士

2006—2012北京大学定量生物学中心  理学博士


工作经历

2012—2016The University of Kansas  博士后

2016—2021华东师范大学化学与分子工程学院  副研究员

2021—今复旦大学药学院药物化学系  副研究员


承担科研项目情况

2018—2020基于计算机蛋白质设计的脂肪酶底物活性改造研究  基金委青年科学基金 主持

2018—2020组蛋白甲基化和去甲基化识别机理的精确计算新方法  基金委重大研究计划培育项目 参与

2019—2022基于深度学习神经网络的膜蛋白序列设计方法  上海市科委自然科学基金探索类项目 主持

2021—2025人工智能驱动的药物分子和蛋白质设计  基金委重点项目 参与


研究方向

人工智能药物设计,生物大分子结构和功能模拟


科研成果

综合采用机器学习和分子模拟等方法,在蛋白结构设计和稳定性预测、蛋白-小分子药物相互作用微观机理和设计、生物大分子模拟等方面取得了创新成果,目前已发表科研论文50余篇,总引用4000余次。


代表性论著

(1)  Xia, W.; He, L.; Bao, J.; Qi, Y.; Zhang, J. Z. H. Insights into Small  Molecule Inhibitor Bindings to PD-L1 with Residue-Specific Binding Free  Energy Calculation. J. Biomol. Struct. Dyn.2021, 0 (0), 1–9.

(2)  Shao, G.; Bao, J.; Pan, X.; He, X.; Qi, Y.; Zhang, J. Z. H.  Computational Analysis of Residue-Specific Binding Free Energies of  Androgen Receptor to Ligands. Front. Mol. Biosci.2021, 8 (March), 1–9.

(3) Huang, D.; Tian, S.; Qi, Y.; Zhang, J. Z. H. Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2. ChemPhysChem2020, 21 (3), 263–271.

(4)  Wang, R.; Cong, Y.; Li, M.; Bao, J.; Qi, Y.; Zhang, J. Z. H. Molecular  Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A  Computational Perspective. Front. Mol. Biosci.2020, 7 (April).

(5)  Qi, Y.; Lee, J.; Cheng, X.; Shen, R.; Islam, S. M.; Roux, B.; Im, W.  CHARMM‐GUI DEER Facilitator for Spin‐pair Distance Distribution  Calculations and Preparation of Restrained‐ensemble Molecular Dynamics  Simulations. J. Comput. Chem.2020, 41 (5), 415–420.

(6)  Li, Z.; Bao, J.; Qi, Y.; Zhang, J. Z. H. Computational Approaches to  Studying Methylated H4K20 Recognition by DNA Repair Factor 53BP1. Phys. Chem. Chem. Phys.2020, 22 (11), 6136–6144.

(7)  Qi, Y.; Zhang, J. Z. H. DenseCPD: Improving the Accuracy of  Neural-Network-Based Computational Protein Sequence Design with  DenseNet. J. Chem. Inf. Model.2020, 60 (3), 1245–1252.

(8)  He, L.; Bao, J.; Yang, Y.; Dong, S.; Zhang, L.; Qi, Y.; Zhang, J. Z. H.  Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational  Alanine Scanning. J. Chem. Inf. Model.2019, 59 (9), 3871–3878.

(9)  Cao, H.; Wang, J.; He, L.; Qi, Y.; Zhang, J. Z. DeepDDG: Predicting the  Stability Change of Protein Point Mutations Using Neural Networks. J. Chem. Inf. Model.2019, 59 (4), 1508–1514.

(10)  Qi, Y.; Lee, J.; Klauda, J. B.; Im, W. CHARMM-GUI Nanodisc Builder for  Modeling and Simulation of Various Nanodisc Systems. J. Comput. Chem.2019, 40 (7), 893–899.

(11) Wang, J.; Cao, H.; Zhang, J. Z. H.; Qi, Y. Computational Protein Design with Deep Learning Neural Networks. Sci. Rep.2018, 8 (1), 1–9.

(12)  Qi, Y.; Lee, J.; Singharoy, A.; McGreevy, R.; Schulten, K.; Im, W.  CHARMM-GUI MDFF/XMDFF Utilizer for Molecular Dynamics Flexible Fitting  Simulations in Various Environments. J. Phys. Chem. B2017, 121 (15), 3718–3723.

(13)  Hsu, P.-C.; Bruininks, B. M. H.; Jefferies, D.; Cesar Telles de Souza,  P.; Lee, J.; Patel, D. S.; Marrink, S. J.; Qi, Y.; Khalid, S.; Im, W.  CHARMM-GUI Martini Maker for Modeling and Simulation of Complex  Bacterial Membranes with Lipopolysaccharides. J. Comput. Chem.2017, 38 (27), 2354–2363.

(14) Qi, Y.; Klauda, J. B.; Im, W. Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues. Biophys. J.2016, 111 (8), 1600–1603.

(15)  Qi, Y.; Ingólfsson, H. I.; Cheng, X.; Lee, J.; Marrink, S. J.; Im, W.  CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini  Force Field. J. Chem. Theory Comput.2015, 11 (9), 4486–4494.

(16)  Qi, Y.; Cheng, X.; Han, W.; Jo, S.; Roux, B.; Schulten, K.; Im, W.  CHARMM-Gui Pace Cg Builder for Solution, Micelle, Bilayer and Vesicle  Simulations. Biophys. J.2015, 106 (2), 809a.

(17) Qi, Y.; Jo, S.; Im, W. Roles of Glycans in Interactions between Gp120 and HIV Broadly Neutralizing Antibodies. Glycobiology2015, 26 (3), 251–260.

(18)  Qi, Y.; Cheng, X.; Lee, J.; Vermaas, J. V.; Pogorelov, T. V.;  Tajkhorshid, E.; Park, S.; Klauda, J. B.; Im, W. CHARMM-GUI HMMM Builder  for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.  Biophys. J.2015, 109 (10), 2012–2022.

(19) Qi, Y.; Im, W. Quantification of Drive-Response Relationships Between Residues During Protein Folding. J. Chem. Theory Comput.2013, 9 (8), 3799–3805.

(20)  Qi, Y.; Wang, Q.; Tang, B.; Lai, L. Identifying Allosteric Binding  Sites in Proteins with a Two-State Gô Model for Novel Allosteric  Effector Discovery. J. Chem. Theory Comput.2012, 8 (8), 2962–2971.

(21)  Qi, Y.; Huang, Y.; Liang, H.; Liu, Z.; Lai, L. Folding Simulations of a  de Novo Designed Protein with a Betaalphabeta Fold. Biophys. J.2010, 98 (2), 321–329.


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