戚逸飞
化学与分子工程学院??????


导航
个人资料
研究方向
开授课程
科研项目
学术成果
荣誉及奖励







个人资料
部门： 化学与分子工程学院
毕业院校：
学位：
学历：
邮编：
联系电话：
传真：
电子邮箱： yfqi@chem.ecnu.edu.cn
办公地址： 中北校区地理馆336
通讯地址：

教育经历
2012年北京大学物理化学博士学位导师：来鲁华教授
2006年北京大学物理学学士学位


工作经历
2016年-华东师范大学化学与分子工程学院专职副研究员
2012年-2016年美国堪萨斯大学计算生物学中心博士后合作导师：Prof. Wonpil Im


个人简介

社会兼职


研究方向
蛋白质设计 生物大分子结构和功能模拟



开授课程


科研项目
主持科研项目:
1. 国家自然科学青年基金基于计算机蛋白质设计的脂肪酶底物活性改造研究2018-2020



学术成果
Wang, J., H. Cao, J. Z. H. Zhang,and Y. Qi. 2018. Computational Protein Design with Deep Learning NeuralNetworks. Sci Rep 8:6349.
Min, D., R. E. Jefferson, Y. Qi,J. Y. Wang, M. A. Arbing, W. Im, and J. U. Bowie. 2018. Unfolding of a ClCchloride transporter retains memory of its evolutionary history. Nat Chem Biol 14:489-496.
Jo, S., D. Myatt, Y. Qi, J.Doutch, L. A. Clifton, W. Im, and G. Widmalm. 2018. Multiple ConformationalStates Contribute to the 3D Structure of a Glucan Decasaccharide: A CombinedSAXS and MD Simulation Study. J Phys Chem B 122:1169-1175.
Patel, D. S., Y. Qi, and W. Im.2017. Modeling and simulation of bacterial outer membranes and interactionswith membrane proteins. Curr Opin Struct Biol 43:131-140.
Machen, A. J., N. Akkaladevi, C.Trecazzi, P. T. O'Neil, S. Mukherjee, Y. Qi, R. Dillard, W. Im, E. P. Gogol, T.A. White, and M. T. Fisher. 2017. Asymmetric Cryo-EM Structure of Anthrax ToxinProtective Antigen Pore with Lethal Factor N-Terminal Domain. Toxins (Basel) 9.
Hsu, P. C., B. M. H. Bruininks, D.Jefferies, P. Cesar Telles de Souza, J. Lee, D. S. Patel, S. J. Marrink, Y. Qi,S. Khalid, and W. Im. 2017. CHARMM-GUI Martini Maker for modeling andsimulation of complex bacterial membranes with lipopolysaccharides. J Comput Chem 38:2354-2363.
Qi, Y., J. Lee, A. Singharoy, R.McGreevy, K. Schulten, and W. Im. 2016. CHARMM-GUI MDFF/xMDFF Utilizer forMolecular Dynamics Flexible Fitting Simulations in Various Environments. J Phys Chem B.
Qi, Y., J. B. Klauda, and W. Im.2016. Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues.Biophys J 111:1600-1603.
Qi, Y., S. Jo, and W. Im. 2016.Roles of glycans in interactions between gp120 and HIV broadly neutralizingantibodies. Glycobiology 26:251-260.
Patel, D. S., S. Re, E. L. Wu, Y.Qi, P. E. Klebba, G. Widmalm, M. S. Yeom, Y. Sugita, and W. Im. 2016. Dynamicsand Interactions of OmpF and LPS: Influence on Pore Accessibility and IonPermeability. Biophys J 110:930-938.
Li, C., X. Teng, Y. Qi, B. Tang,H. Shi, X. Ma, and L. Lai. 2016. Conformational Flexibility of a Short Loopnear the Active Site of the SARS-3CLpro is Essential to Maintain CatalyticActivity. Sci Rep 6:20918.
Lee, J., X. Cheng, J. M. Swails,M. S. Yeom, P. K. Eastman, J. A. Lemkul, S. Wei, J. Buckner, J. C. Jeong, Y.Qi, S. Jo, V. S. Pande, D. A. Case, C. L. Brooks, 3rd, A. D. MacKerell, Jr., J.B. Klauda, and W. Im. 2016. CHARMM-GUI Input Generator for NAMD, GROMACS,AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive ForceField. J Chem Theory Comput 12:405-413.
Kumar, R., Y. Qi, H. Matsumura,S. Lovell, H. Yao, K. P. Battaile, W. Im, P. Moenne-Loccoz, and M. Rivera.2016. Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonasaeruginosa Causes Closure of the H32 Loop in the Apo-Protein. Biochemistry55:2622-2631.
Jo, S., Y. Qi, and W. Im. 2016.Preferred conformations of N-glycan core pentasaccharide in solution and inglycoproteins. Glycobiology 26:19-29.
Jo, S., X. Cheng, J. Lee, S. Kim,S. J. Park, D. S. Patel, A. H. Beaven, K. I. Lee, H. Rui, S. Park, H. S. Lee,B. Roux, A. D. MacKerell, Jr., J. B. Klauda, Y. Qi, and W. Im. 2016. CHARMM-GUI10 years for biomolecular modeling and simulation. J Comput Chem.
Fleming, P. J., D. S. Patel, E.L. Wu, Y. Qi, M. S. Yeom, M. C. Sousa, K. G. Fleming, and W. Im. 2016. BamAPOTRA Domain Interacts with a Native Lipid Membrane Surface. Biophys J 110:2698-2709.
Wu, E. L., Y. Qi, S. Park, S. S.Mallajosyula, A. D. MacKerell, Jr., J. B. Klauda, and W. Im. 2015. Insight intoEarly-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophys J 109:2090-2100.
Qi, Y., H. I. Ingolfsson, X.Cheng, J. Lee, S. J. Marrink, and W. Im. 2015. CHARMM-GUI Martini Maker forCoarse-Grained Simulations with the Martini Force Field. J Chem Theory Comput 11:4486-4494.
Qi, Y., X. Cheng, J. Lee, J. V.Vermaas, T. V. Pogorelov, E. Tajkhorshid, S. Park, J. B. Klauda, and W. Im.2015. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly MobileMembrane-Mimetic Model. Biophys J 109:2012-2022.
Ma, X., Y. Qi, and L. Lai. 2015.Allosteric sites can be identified based on the residue-residue interactionenergy difference. Proteins 83:1375-1384.
Lee, H. S., Y. Qi, and W. Im.2015. Effects of N-glycosylation on protein conformation and dynamics: ProteinData Bank analysis and molecular dynamics simulation study. Sci Rep 5:8926.
Cheng, X., S. Jo, Y. Qi, F. M.Marassi, and W. Im. 2015. Solid-State NMR-Restrained Ensemble Dynamics of aMembrane Protein in Explicit Membranes. Biophys J 108:1954-1962.
Wu, E. L., Y. Qi, K. C. Song, J.B. Klauda, and W. Im. 2014. Preferred orientations of phosphoinositides inbilayers and their implications in protein recognition mechanisms. J Phys ChemB 118:4315-4325.
Wu, E. L., X. Cheng, S. Jo, H.Rui, K. C. Song, E. M. Davila-Contreras, Y. Qi, J. Lee, V. Monje-Galvan, R. M.Venable, J. B. Klauda, and W. Im. 2014. CHARMM-GUI Membrane Builder towardrealistic biological membrane simulations. J Comput Chem 35:1997-2004.
Wang, Q., Y. Qi, N. Yin, and L.Lai. 2014. Discovery of novel allosteric effectors based on the predictedallosteric sites for Escherichia coli D-3-phosphoglycerate dehydrogenase. PLoS One 9:e94829.
Qi, Y., X. Cheng, W. Han, S. Jo,K. Schulten, and W. Im. 2014. CHARMM-GUI PACE CG Builder for solution, micelle,and bilayer coarse-grained simulations. J Chem Inf Model 54:1003-1009.
Jo, S., X. Cheng, S. M. Islam, L.Huang, H. Rui, A. Zhu, H. S. Lee, Y. Qi, W. Han, K. Vanommeslaeghe, A. D.MacKerell, Jr., B. Roux, and W. Im. 2014. CHARMM-GUI PDB manipulator foradvanced modeling and simulations of proteins containing nonstandard residues. Adv Protein Chem Struct Biol 96:235-265.
Jeong, J. C., S. Jo, E. L. Wu, Y.Qi, V. Monje-Galvan, M. S. Yeom, L. Gorenstein, F. Chen, J. B. Klauda, and W.Im. 2014. ST-analyzer: a web-based user interface for simulation trajectoryanalysis. J Comput Chem 35:957-963.
Qi, Y., and W. Im. 2013.Quantification of Drive-Response Relationships Between Residues During ProteinFolding. J Chem Theory Comput 9.
Qi, Y., Q. Wang, B. Tang, and L.Lai. 2012. Identifying Allosteric Binding Sites in Proteins with a Two-State GoModel for Novel Allosteric Effector Discovery. J Chem Theory Comput 8:2962-2971.
Qi, Y., H. Liang, X. Han, and L.Lai. 2012. Sequence preference of alpha-helix N-terminal tetrapeptide. ProteinPept Lett 19:345-352.
Qi, Y., Y. Huang, H. Liang, Z.Liu, and L. Lai. 2010. Folding simulations of a de novo designed protein with abetaalphabeta fold. Biophys J 98:321-329.
Li, C., Y. Qi, X. Teng, Z. Yang,P. Wei, C. Zhang, L. Tan, L. Zhou, Y. Liu, and L. Lai. 2010. Maturationmechanism of severe acute respiratory syndrome (SARS) coronavirus 3C-likeproteinase. J Biol Chem 285:28134-28140.


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