Professor | Yi-Fei Qi | Asia Growth Partners

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Name	Yi-Fei Qi
Contact Information	yfqi@fudan.edu.cn
Language ability	Chinese, English
Province	Shanghai

Upload Avatar (500 x 500)

Name

Yi-Fei Qi

Contact Information

yfqi@fudan.edu.cn

Language ability

Chinese, English

Province

Shanghai

University/Lab Affiliation and Title	Fudan University
Faculty	Pharmaceutical Sciences
Academic Background & Achievements	2002-2006 Bachelor of Science: Peking University, School of Physics 2006-2012 Ph.D. in Science: Peking University, Center for Quantitative Biology Published over 60 research papers with more than 8000 citations on Google Scholar
Work Experience	2012-2016 - The University of Kansas - Postdoctoral Researcher 2016-2021 - East China Normal University, School of Chemistry and Molecular Engineering - Associate Researcher 2021-Present - Fudan University, School of Pharmacy, Department of Medicinal Chemistry - Associate Researcher
Awards	2018-2020 National Natural Science Foundation of China Youth Science Fund - Principal Investigator 2019-2022 Shanghai Science and Technology Committee Natural Science Foundation Exploration Project - Principal Investigator

University/Lab Affiliation and Title

Fudan University

Faculty

Pharmaceutical Sciences

Academic Background & Achievements

2002-2006 Bachelor of Science: Peking University, School of Physics
2006-2012 Ph.D. in Science: Peking University, Center for Quantitative Biology
Published over 60 research papers with more than 8000 citations on Google Scholar

Work Experience

2012-2016 - The University of Kansas - Postdoctoral Researcher
2016-2021 - East China Normal University, School of Chemistry and Molecular Engineering - Associate Researcher
2021-Present - Fudan University, School of Pharmacy, Department of Medicinal Chemistry - Associate Researcher

Awards

2018-2020 National Natural Science Foundation of China Youth Science Fund - Principal Investigator
2019-2022 Shanghai Science and Technology Committee Natural Science Foundation Exploration Project - Principal Investigator

Areas of Focus	Artificial intelligence in protein and small molecule drug design Simulation of biomolecular structure and function
Publications	Insights into Small Molecule Inhibitor Bindings to PD-L1 with Residue-Specific Binding Free Energy Calculation, Xia, W.; He, L.; Bao, J.; Qi, Y.; Zhang, J. Z. H., 2021 Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands, Shao, G.; Bao, J.; Pan, X.; He, X.; Qi, Y.; Zhang, J. Z. H., 2021 Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2, Huang, D.; Tian, S.; Qi, Y.; Zhang, J. Z. H., 2020 Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective, Wang, R.; Cong, Y.; Li, M.; Bao, J.; Qi, Y.; Zhang, J. Z. H., 2020 CHARMM‐GUI DEER Facilitator for Spin‐pair Distance Distribution Calculations and Preparation of Restrained‐ensemble Molecular Dynamics Simulations, Qi, Y.; Lee, J.; Cheng, X.; Shen, R.; Islam, S. M.; Roux, B.; Im, W., 2020 Computational Approaches to Studying Methylated H4K20 Recognition by DNA Repair Factor 53BP1, Li, Z.; Bao, J.; Qi, Y.; Zhang, J. Z. H., 2020 DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet, Qi, Y.; Zhang, J. Z. H., 2020 Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning, He, L.; Bao, J.; Yang, Y.; Dong, S.; Zhang, L.; Qi, Y.; Zhang, J. Z. H., 2019 DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks, Cao, H.; Wang, J.; He, L.; Qi, Y.; Zhang, J. Z., 2019 CHARMM-GUI Nanodisc Builder for Modeling and Simulation of Various Nanodisc Systems, Qi, Y.; Lee, J.; Klauda, J. B.; Im, W., 2019 Computational Protein Design with Deep Learning Neural Networks, Wang, J.; Cao, H.; Zhang, J. Z. H.; Qi, Y., 2018 CHARMM-GUI MDFF/XMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments, Qi, Y.; Lee, J.; Singharoy, A.; McGreevy, R.; Schulten, K.; Im, W., 2017 CHARMM-GUI Martini Maker for Modeling and Simulation of Complex Bacterial Membranes with Lipopolysaccharides, 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., 2017 Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues, Qi, Y.; Klauda, J. B.; Im, W., 2016 CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field, Qi, Y.; Ingólfsson, H. I.; Cheng, X.; Lee, J.; Marrink, S. J.; Im, W., 2015 CHARMM-Gui Pace Cg Builder for Solution, Micelle, Bilayer and Vesicle Simulations, Qi, Y.; Cheng, X.; Han, W.; Jo, S.; Roux, B.; Schulten, K.; Im, W., 2015 Roles of Glycans in Interactions between Gp120 and HIV Broadly Neutralizing Antibodies, Qi, Y.; Jo, S.; Im, W., 2015 CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model, Qi, Y.; Cheng, X.; Lee, J.; Vermaas, J. V.; Pogorelov, T. V.; Tajkhorshid, E.; Park, S.; Klauda, J. B.; Im, W., 2015 Quantification of Drive-Response Relationships Between Residues During Protein Folding, Qi, Y.; Im, W., 2013 Identifying Allosteric Binding Sites in Proteins with a Two-State Gô Model for Novel Allosteric Effector Discovery, Qi, Y.; Wang, Q.; Tang, B.; Lai, L., 2012 Folding Simulations of a de Novo Designed Protein with a Betaalphabeta Fold, Qi, Y.; Huang, Y.; Liang, H.; Liu, Z.; Lai, L., 2010

Areas of Focus

Artificial intelligence in protein and small molecule drug design
Simulation of biomolecular structure and function

Publications

Insights into Small Molecule Inhibitor Bindings to PD-L1 with Residue-Specific Binding Free Energy Calculation, Xia, W.; He, L.; Bao, J.; Qi, Y.; Zhang, J. Z. H., 2021
Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands, Shao, G.; Bao, J.; Pan, X.; He, X.; Qi, Y.; Zhang, J. Z. H., 2021
Binding Modes of Small‐Molecule Inhibitors to the EED Pocket of PRC2, Huang, D.; Tian, S.; Qi, Y.; Zhang, J. Z. H., 2020
Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective, Wang, R.; Cong, Y.; Li, M.; Bao, J.; Qi, Y.; Zhang, J. Z. H., 2020
CHARMM‐GUI DEER Facilitator for Spin‐pair Distance Distribution Calculations and Preparation of Restrained‐ensemble Molecular Dynamics Simulations, Qi, Y.; Lee, J.; Cheng, X.; Shen, R.; Islam, S. M.; Roux, B.; Im, W., 2020
Computational Approaches to Studying Methylated H4K20 Recognition by DNA Repair Factor 53BP1, Li, Z.; Bao, J.; Qi, Y.; Zhang, J. Z. H., 2020
DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet, Qi, Y.; Zhang, J. Z. H., 2020
Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning, He, L.; Bao, J.; Yang, Y.; Dong, S.; Zhang, L.; Qi, Y.; Zhang, J. Z. H., 2019
DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks, Cao, H.; Wang, J.; He, L.; Qi, Y.; Zhang, J. Z., 2019
CHARMM-GUI Nanodisc Builder for Modeling and Simulation of Various Nanodisc Systems, Qi, Y.; Lee, J.; Klauda, J. B.; Im, W., 2019
Computational Protein Design with Deep Learning Neural Networks, Wang, J.; Cao, H.; Zhang, J. Z. H.; Qi, Y., 2018
CHARMM-GUI MDFF/XMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments, Qi, Y.; Lee, J.; Singharoy, A.; McGreevy, R.; Schulten, K.; Im, W., 2017
CHARMM-GUI Martini Maker for Modeling and Simulation of Complex Bacterial Membranes with Lipopolysaccharides, 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., 2017
Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues, Qi, Y.; Klauda, J. B.; Im, W., 2016
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field, Qi, Y.; Ingólfsson, H. I.; Cheng, X.; Lee, J.; Marrink, S. J.; Im, W., 2015
CHARMM-Gui Pace Cg Builder for Solution, Micelle, Bilayer and Vesicle Simulations, Qi, Y.; Cheng, X.; Han, W.; Jo, S.; Roux, B.; Schulten, K.; Im, W., 2015
Roles of Glycans in Interactions between Gp120 and HIV Broadly Neutralizing Antibodies, Qi, Y.; Jo, S.; Im, W., 2015
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model, Qi, Y.; Cheng, X.; Lee, J.; Vermaas, J. V.; Pogorelov, T. V.; Tajkhorshid, E.; Park, S.; Klauda, J. B.; Im, W., 2015
Quantification of Drive-Response Relationships Between Residues During Protein Folding, Qi, Y.; Im, W., 2013
Identifying Allosteric Binding Sites in Proteins with a Two-State Gô Model for Novel Allosteric Effector Discovery, Qi, Y.; Wang, Q.; Tang, B.; Lai, L., 2012
Folding Simulations of a de Novo Designed Protein with a Betaalphabeta Fold, Qi, Y.; Huang, Y.; Liang, H.; Liu, Z.; Lai, L., 2010

Ai Protein Design Small Molecule Drug Design Biomolecular Simulation Structure Prediction Stability Prediction Molecular Interaction Machine Learning Molecular Dynamics

Xian Zeng - Fudan University

Rong Sheng - Zhejiang University

Xiaowu Dong - Zhejiang University

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