Pengfei Li

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 39

Top Venues

Journal of chemical information and modeling

Journal of chemical theory and computation

Biochemistry

Journal of the American Chemical Society

Loyola University Chicago

Michigan State University (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Loyola University Chicago Aug 10 2020

United States

Assistant Professor :: Chemistry and Biochemistry

Yale University Jan 01 2018 - Aug 09 2020

United States

Postdoctoral Associate :: Chemistry

University of Illinois at Urbana-Champaign Sep 01 2016 - Dec 31 2017

United States

Postdoctoral Research Associate :: Chemistry

Michigan State University

United States

Graduate Assistant :: Chemistry

University of Florida Aug 22 2011

United States

Graduate Assistant :: Chemistry

Education History

Michigan State University

United States

PHD :: Chemistry

University of Florida

United States

PHD :: Chemistry

Publications

Luke Landry, Pengfei Li
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. Journal of chemical information and modeling 64 (3) (2024)
Zhen Li, Subhamoy Bhowmik, Luca Sagresti, Giuseppe Brancato, Madelyn Smith, David E Benson, Pengfei Li, Kenneth M Merz
Simulating Metal-Imidazole Complexes. Journal of chemical theory and computation 20 (15) (2024)
Luke Landry, Pengfei Li
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. Journal of chemical information and modeling (2024)
Zhen Li, Subhamoy Bhowmik, Luca Sagresti, Giuseppe Brancato, Madelyn Smith, David E Benson, Pengfei Li, Kenneth M Merz
Simulating Metal-Imidazole Complexes. Journal of chemical theory and computation 20 (15) (2024)
Zhen Li, Subhamoy Bhowmik, Luca Sagresti, Giuseppe Brancato, Madelyn Smith, David E Benson, Pengfei Li, Kenneth M Merz
Simulating Metal-Imidazole Complexes. Journal of chemical theory and computation 20 (15) (2024)
Luke Landry, Pengfei Li
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. Journal of chemical information and modeling 64 (3) (2024)
Zhen Li, Subhamoy Bhowmik, Luca Sagresti, Giuseppe Brancato, Madelyn Smith, David E Benson, Pengfei Li, Kenneth M Merz
Simulating Metal-Imidazole Complexes. Journal of chemical theory and computation (2024)
Luke Landry, Pengfei Li
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. Journal of chemical information and modeling 64 (3) (2024)
Luke Landry, Pengfei Li
Development of a Fluctuating Charge Model for Zinc-Containing Metalloproteins. Journal of chemical information and modeling 64 (3) (2024)
Wenhan Fang, Shishi Feng, Zhihui Jiang, WanZhen Liang, Pengfei Li, Binju Wang
Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase. JACS Au 3 (2) (2023)
Theodore Gerard, Yang Wei, Erwin Weerawardhana, Adriana Lugosan, Matthias Zeller, Diane A Dickie, Pengfei Li, Wei Tsung Lee
An Inorganic Fluorescent Chemosensor: Rational Design and Selective Mg 2+ Detection. ACS omega 8 (4) (2023)
Ajay Sharma, Chris Whittington, Mohammed A Jabed, S Gage Hill, Anastasiia Kostenko, Tao Yu, Pengfei Li, Peter E Doan, Brian M Hoffman, Adam R Offenbacher
13 C Electron Nuclear Double Resonance Spectroscopy-Guided Molecular Dynamics Computations Reveal the Structure of the Enzyme-Substrate Complex of an Active, N -Linked Glycosylated Lipoxygenase. Biochemistry 62 (10) (2023)
Madelyn Smith, Zhen Li, Luke Landry, Kenneth M Merz, Pengfei Li
Consequences of Overfitting the van der Waals Radii of Ions. Journal of chemical theory and computation (2023)
Ajay Sharma, Chris Whittington, Mohammed A Jabed, S Gage Hill, Anastasiia Kostenko, Tao Yu, Pengfei Li, Peter E Doan, Brian M Hoffman, Adam R Offenbacher
13 C Electron Nuclear Double Resonance Spectroscopy-Guided Molecular Dynamics Computations Reveal the Structure of the Enzyme-Substrate Complex of an Active, N -Linked Glycosylated Lipoxygenase. Biochemistry 62 (10) (2023)
David A Case, Hasan Metin Aktulga, Kellon Belfon, David S Cerutti, Gerardo Andrés Cisneros, Vinícius Wilian D Cruzeiro, Negin Forouzesh, Timothy J Giese, Andreas W Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R Machado, Hai Minh Nguyen, Kurt A O'Hearn, Alexey V Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E Cheatham, Daniel R Roe, Adrian E Roitberg, Carlos L Simmerling, Darrin M York, Maria C Nagan, Kenneth M Merz
AmberTools. Journal of chemical information and modeling (2023)
Dong Fang, Zhiyang Zhang, Jihang Zhai, Baolin Guo, Pengfei Li, Xiaoyuan Liu, Jin-Shuai Song, Songqiang Xie, Ruibo Wu, Yuan Zhao, Chaojie Wang
Enzymatic-related network of catalysis, polyamine, and tumors for acetylpolyamine oxidase: from calculation to experiment. Chemical science 15 (8) (2023)
Wenhan Fang, Shishi Feng, Zhihui Jiang, WanZhen Liang, Pengfei Li, Binju Wang
Understanding the Key Roles of pH Buffer in Accelerating Lignin Degradation by Lignin Peroxidase. JACS Au 3 (2) (2023)
Ajay Sharma, Chris Whittington, Mohammed A Jabed, S Gage Hill, Anastasiia Kostenko, Tao Yu, Pengfei Li, Peter E Doan, Brian M Hoffman, Adam R Offenbacher
13 C Electron Nuclear Double Resonance Spectroscopy-Guided Molecular Dynamics Computations Reveal the Structure of the Enzyme-Substrate Complex of an Active, N -Linked Glycosylated Lipoxygenase. Biochemistry (2023)
Dong Fang, Zhiyang Zhang, Jihang Zhai, Baolin Guo, Pengfei Li, Xiaoyuan Liu, Jin-Shuai Song, Songqiang Xie, Ruibo Wu, Yuan Zhao, Chaojie Wang
Enzymatic-related network of catalysis, polyamine, and tumors for acetylpolyamine oxidase: from calculation to experiment. Chemical science 15 (8) (2023)
Theodore Gerard, Yang Wei, Erwin Weerawardhana, Adriana Lugosan, Matthias Zeller, Diane A Dickie, Pengfei Li, Wei Tsung Lee
An Inorganic Fluorescent Chemosensor: Rational Design and Selective Mg 2+ Detection. ACS omega 8 (4) (2023)
Xiaoyue Yang, Shaohui Liu, Zhili Yin, Mengguo Chen, Jin-Shuai Song, Pengfei Li, Long-Hua Yang
New insights into the proton pumping mechanism of ba 3 cytochrome c oxidase: the functions of key residues and water. Physical chemistry chemical physics : PCCP (2023)
Madelyn Smith, Pengfei Li
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. Journal of chemical information and modeling 63 (1) (2022)
Madelyn Smith, Pengfei Li
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. Journal of chemical information and modeling 63 (1) (2022)
Madelyn Smith, Pengfei Li
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. Journal of chemical information and modeling 63 (1) (2022)
Madelyn Smith, Pengfei Li
Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. Journal of chemical information and modeling (2022)
Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M Merz
Correction to "Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models". Journal of chemical information and modeling 61 (7) (2021)
Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M Merz
Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. Journal of chemical theory and computation 17 (4) (2021)
Andrew J Veenis, Pengfei Li, Alexander V Soudackov, Sharon Hammes-Schiffer, Philip C Bevilacqua
Investigation of the pKa of the Nucleophilic O2' of the Hairpin Ribozyme. The journal of physical chemistry. B 125 (43) (2021)
Arkajyoti Sengupta, Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M Merz
Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. Journal of chemical information and modeling 61 (2) (2021)
Joshua J Goings, Pengfei Li, Qiwen Zhu, Sharon Hammes-Schiffer
Formation of an unusual glutamine tautomer in a blue light using flavin photocycle characterizes the light-adapted state. Proceedings of the National Academy of Sciences of the United States of America 117 (43) (2020)
Zhen Li, Lin Frank Song, Pengfei Li, Kenneth M Merz
Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. Journal of chemical theory and computation 16 (7) (2020)
Pengfei Li, Alexander V Soudackov, Brian Koronkiewicz, James M Mayer, Sharon Hammes-Schiffer
Theoretical Study of Shallow Distance Dependence of Proton-Coupled Electron Transfer in Oligoproline Peptides. Journal of the American Chemical Society 142 (32) (2020)
Pengfei Li, Atul Rangadurai, Hashim M Al-Hashimi, Sharon Hammes-Schiffer
Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. Journal of the American Chemical Society 142 (25) (2020)
Clorice R Reinhardt, Pengfei Li, Gyunghoon Kang, JoAnne Stubbe, Catherine L Drennan, Sharon Hammes-Schiffer
Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase. Journal of the American Chemical Society 142 (32) (2020)
Pengfei Li, Alexander V Soudackov, Sharon Hammes-Schiffer
Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations. Journal of the American Chemical Society 140 (8) (2018)
Pengfei Li, Alexander V Soudackov, Sharon Hammes-Schiffer
Impact of Mutations on the Binding Pocket of Soybean Lipoxygenase: Implications for Proton-Coupled Electron Transfer. The journal of physical chemistry letters 9 (22) (2018)
Zhuoqin Yu, Pengfei Li, Kenneth M Merz
Using Ligand-Induced Protein Chemical Shift Perturbations To Determine Protein-Ligand Structures. Biochemistry 56 (18) (2017)
Zhuoqin Yu, Pengfei Li, Kenneth M Merz
Extended Zinc AMBER Force Field (EZAFF). Journal of chemical theory and computation 14 (1) (2017)
Pengfei Li, Kenneth M Merz
Metal Ion Modeling Using Classical Mechanics. Chemical reviews 117 (3) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Pengfei Li