Jun Gao-College of Informatics

Name

Jun Gao

Sex

Male

Title

Professor

Institute

College of Informatics, Huazhong Agricultural University

Address

1st Shizishan Road, Hongshan, Wuhan 430070, China

Email

gaojun@mail.hzau.edu.cn

Fax

Research Interest

Multiscale computational models of complex biological systems; High performance parallel computational simulation of biological systems ; Drug discovery and precision medicine

Academic activities

Education and research experience

EDUCATION

Ph.D. Shandong University Jinan, Shandong, P. R. China 1999-2005

Doctor of Sciences, Physical Chemistry

B.S. Shandong University Jinan, Shandong, P. R. China 1993-1997

Bachelor of Sciences, Environmental Engineering

EXPERIENCE

Professor in Computational Biochemistry

College of Informatics, Huazhong Agricultural University, P. R. China 2014~

Associate Professor 2009~ 2014

School of Chemistry and Chemical Engineering, Shandong University, P. R. China

Post-doctoral Research Fellowship 2006-2009

Department of Bioinformatics and Computer Science, University of Sciences in Philadelphia

West Center for Computational Chemistry and Drug Design, University of Sciences in Philadelphia

Ph.D. Research Assistant 1999-2005

Institute of Theoretical and Computational Chemistry, Beijing University, P. R. China 2002-2005

School of Chemistry and Chemical Engineering, Shandong University, P. R. China 1999-2002

Grants (Government-funded)

A QM/MM-TDDFT study on reaction mechanism of cysteine dioxygenase, (Grant number: 21373124), National Natural Science Foundation of China, 2014-2017.

Multi Spin States Updateable Charge Force Filed for Heme Models, (Grant number: 21873034

), National Natural Science Foundation of China, 2019-2022.

Ab initio molecular dynamics method and calculation program based on task parallel,(Grant number:2017EFB0203405), National Key R&D Program of China, 2018-2021

Representative publications（*for corresponding authors, # for first authors）

1.Zhou, J.; Fang, L.; Yang, Z.; Xu, S.; Lv, M.; Sun, Z.; Chen, J.; Wang, D.; Gao*, J.; Xiao*, S., Identification of novel proteolytically inactive mutations in coronavirus 3C-like protease using a combined approach. The FASEB Journal 2019.

2.Li, Q.; Xiong, L.; Gao*, J.; Zhang*, H.-Y., Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors. J Mol Model 2019, 25 (8), 246.

3.Li, G.; Quan, Y.; Wang, X.; Liu, R.; Bie, L.; Gao*, J.; Zhang, H.-Y., Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs. Frontiers in Chemistry 2019, 6, 666.

4.Du*, L.; Liu, F.; Li, Y.; Yang, Z.; Zhang, Q.; Zhu, C.; Gao*, J., Dioxygen Activation by Iron Complexes: The Catalytic Role of Intersystem Crossing Dynamics for a Heme-Related Model. The Journal of Physical Chemistry C 2018, 122 (5), 2821-2831.

5.Bie, L.; Du, L.; Yuan*, Q.; Gao*, J., How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study. Journal of Molecular Modeling 2018, 24 (7), 159.

6.Liu, F.; Du*, L.; Zhang, D.; Gao*, J., Direct Learning Hidden Excited State Interaction Patterns from ab initio Dynamics and Its Implication as Alternative Molecular Mechanism Models. Sci Rep 2017, 7 (1), 8737.

7.Liu, F.; Du*, L.; Lan, Z.; Gao*, J., Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens. Photochemical & Photobiological Sciences 2017, 16, 211-219.

8.Zhu, W.; Xiong, L.; Peng, J.; Deng, X.; Gao*, J.; Li*, C.-m., Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers. Scientific Reports 2016, 6, 37680.

9.Zhu, W.; Xiong, L.; Peng, J.; Deng, X.; Gao*, J.; Li*, C.-m., Structure-Dependent Membrane-Perturbing Potency of Four Proanthocyanidin Dimers on 3T3-L1 Preadipocytes. Journal of Agricultural and Food Chemistry 2016, 64 (37), 7022-7032.

10.Zhao, H.; Fang*, C.; Gao*, J.; Liu, C., Spin-state energies of heme-related models from spin-flip TDDFT calculations. Phys. Chem. Chem. Phys. 2016, 18 (42), 29486-29494.

11.Liu, F.; Du*, L.; Zhang, D.; Gao*, J., Performance of density functional theory on the anisotropic halogen···halogen interactions and potential energy surface: Problems and possible solutions. International Journal of Quantum Chemistry 2016, 116 (9), 710-717.

12.Wang, Q.; Gao*, J.; Zhang, D.; Liu, C., A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism. Chemical Physics 2015, 450–451 (0), 1-11.

13.Liu, F.; Du*, L.; Gao*, J.; Wang, L.; Song, B.; Liu, C., Application of polarizable ellipsoidal force field model to pnicogen bonds. Journal of Computational Chemistry 2015, 36 (7), 441-448.

14.Wang, L.; Gao*, J.; Bi, F.; Song, B.; Liu, C., Toward the Development of the Potential with Angular Distortion for Halogen Bond: A Comparison of Potential Energy Surfaces between Halogen Bond and Hydrogen Bond. The Journal of Physical Chemistry A 2014, 118 (39), 9140-9147.

15.Wang, L.; Che, X.; Li, H.; Gao*, J.; Liu, C., Theoretical study on the working mechanism of a reversible light-driven rotary molecular motor. Theoretical Chemistry Accounts 2014, 133 (10), 1-8.

16.Shen, L.; Chen, Y.; Li*, X.; Gao*, J., Effects of Substituents on Tetracene Derivatives on Their Stabilities and Singlet Fission. Journal of Molecular Graphics and Modelling 2014, 51 (0), 86-96.

17.Che, X.; Gao*, J.; Liu, Y.; Liu, C., Metal vs. chalcogen competition in the catalytic mechanism of cysteine dioxygenase. Journal of Inorganic Biochemistry 2013, 122 (0), 1-7.

18.Che, X.; Gao*, J.; Du, L.; Liu*, C., Theoretical Investigation of the High-Spin "Fe-Proximal Oxygen" Catalytic Mechanism of Rat Cysteine Dioxygenase. J Theor Comput Chem 2013, 12 (3), 1350001-10.

19.Bi, F.; Gao*, J.; Wang, L.; Du, L.; Song, B.; Liu, C., Polarization-enhanced bonding process of halogen bond, a theoretical study on F–H/F–X (X;=F,Cl,Br;I) and ammonia. Chemical Physics 2013, 426 (0), 16-22.

20.Wang, Q.; Gao^*,J.; Liu, Y.; Liu^*,C., Molecular dynamics simulation of the interaction between protein tyrosine phosphatase 1B and aryl diketoacid derivatives. Journal of Molecular Graphics and Modelling 2012, 38 (0), 186-193.

21.Gao, J.; Li^*,Z.; Russell, T.; Li, Z., Antibody affinity purification using metallic nickel particles. Journal of Chromatography B 2012, 895–896 (0), 89-93.

22.Che, X.; Gao*, J.; Zhang, D.; Liu*, C., How Do the Thiolate Ligand and its Relative Position Control the Oxygen Activation in the Cysteine Dioxygenase Model? Journal of Physical Chemistry A 2012, 116, 5510-5517.

23.Gao, J.; Li, Z., Uncover the conserved property underlying sequence-distant and structure-similar proteins. Biopolymers 2010, 93 (4), 340-347.

24.Gao, J.; Li, Z., Comparing four different approaches for the determination of inter-residue interactions provides insight for the structure prediction of helical membrane proteins. Biopolymers 2009, 91 (7), 547-556.

25.Gao, J.; Li, Z., Inter-residue interactions in protein structures exhibit power-law behavior. Biopolymers 2008, 89 (12), 1174-178.

26.Gao, J.; Li, Z., Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone. Journal of Computer-Aided Molecular Design 2008, 23 (11), 755-763.

27.Gao, J.; Zou, W.; Liu, W.; Xiao, Y.; Peng, D.; Song, B.; Liu, C., Time-dependent four-component relativistic density-functional theory for excitation energies. II. The exchange-correlation kernel. Journal of Chemical Physics 2005, 123 (5), 054102

28.Gao, J.; Liu, W.; Song, B.; Liu, C., Time-dependent four-component relativistic density functional theory for excitation energies. Journal of Chemical Physics 2004, 121 (14), 6658.

Basic Information
Name	Jun Gao		Sex	Male	Title	Professor
Institute		College of Informatics, Huazhong Agricultural University
Address		1st Shizishan Road, Hongshan, Wuhan 430070, China
Email		gaojun@mail.hzau.edu.cn
Fax
Research Interest
Multiscale computational models of complex biological systems; High performance parallel computational simulation of biological systems ; Drug discovery and precision medicine
Academic activities

Education and research experience
EDUCATION Ph.D. Shandong University Jinan, Shandong, P. R. China 1999-2005 Doctor of Sciences, Physical Chemistry B.S. Shandong University Jinan, Shandong, P. R. China 1993-1997 Bachelor of Sciences, Environmental Engineering EXPERIENCE Professor in Computational Biochemistry College of Informatics, Huazhong Agricultural University, P. R. China 2014~ Associate Professor 2009~ 2014 School of Chemistry and Chemical Engineering, Shandong University, P. R. China Post-doctoral Research Fellowship 2006-2009 Department of Bioinformatics and Computer Science, University of Sciences in Philadelphia West Center for Computational Chemistry and Drug Design, University of Sciences in Philadelphia Ph.D. Research Assistant 1999-2005 Institute of Theoretical and Computational Chemistry, Beijing University, P. R. China 2002-2005 School of Chemistry and Chemical Engineering, Shandong University, P. R. China 1999-2002
Grants (Government-funded)
A QM/MM-TDDFT study on reaction mechanism of cysteine dioxygenase, (Grant number: 21373124), National Natural Science Foundation of China, 2014-2017. Multi Spin States Updateable Charge Force Filed for Heme Models, (Grant number: 21873034 ), National Natural Science Foundation of China, 2019-2022. Ab initio molecular dynamics method and calculation program based on task parallel,(Grant number:2017EFB0203405), National Key R&D Program of China, 2018-2021
Representative publications（*for corresponding authors, # for first authors）
1.Zhou, J.; Fang, L.; Yang, Z.; Xu, S.; Lv, M.; Sun, Z.; Chen, J.; Wang, D.; Gao, J.; Xiao, S., Identification of novel proteolytically inactive mutations in coronavirus 3C-like protease using a combined approach. The FASEB Journal 2019. 2.Li, Q.; Xiong, L.; Gao, J.; Zhang, H.-Y., Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors. J Mol Model 2019, 25 (8), 246. 3.Li, G.; Quan, Y.; Wang, X.; Liu, R.; Bie, L.; Gao, J.; Zhang, H.-Y., Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs. Frontiers in Chemistry* 2019, 6, 666. 4.Du, L.; Liu, F.; Li, Y.; Yang, Z.; Zhang, Q.; Zhu, C.; Gao, J., Dioxygen Activation by Iron Complexes: The Catalytic Role of Intersystem Crossing Dynamics for a Heme-Related Model. The Journal of Physical Chemistry C 2018, 122 (5), 2821-2831. 5.Bie, L.; Du, L.; Yuan, Q.; Gao, J., How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study. Journal of Molecular Modeling 2018, 24 (7), 159. 6.Liu, F.; Du, L.; Zhang, D.; Gao, J., Direct Learning Hidden Excited State Interaction Patterns from ab initio Dynamics and Its Implication as Alternative Molecular Mechanism Models. Sci Rep 2017, 7 (1), 8737. 7.Liu, F.; Du, L.; Lan, Z.; Gao, J., Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens. Photochemical & Photobiological Sciences 2017, 16, 211-219. 8.Zhu, W.; Xiong, L.; Peng, J.; Deng, X.; Gao, J.; Li, C.-m., Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers. Scientific Reports 2016, 6, 37680. 9.Zhu, W.; Xiong, L.; Peng, J.; Deng, X.; Gao, J.; Li, C.-m., Structure-Dependent Membrane-Perturbing Potency of Four Proanthocyanidin Dimers on 3T3-L1 Preadipocytes. Journal of Agricultural and Food Chemistry 2016, 64 (37), 7022-7032. 10.Zhao, H.; Fang, C.; Gao, J.; Liu, C., Spin-state energies of heme-related models from spin-flip TDDFT calculations. Phys. Chem. Chem. Phys. 2016, 18 (42), 29486-29494. 11.Liu, F.; Du, L.; Zhang, D.; Gao, J., Performance of density functional theory on the anisotropic halogen···halogen interactions and potential energy surface: Problems and possible solutions. International Journal of Quantum Chemistry 2016, 116 (9), 710-717. 12.Wang, Q.; Gao, J.; Zhang, D.; Liu, C., A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism. Chemical Physics* 2015, 450–451 (0), 1-11. 13.Liu, F.; Du, L.; Gao, J.; Wang, L.; Song, B.; Liu, C., Application of polarizable ellipsoidal force field model to pnicogen bonds. Journal of Computational Chemistry 2015, 36 (7), 441-448. 14.Wang, L.; *Gao, J.*; Bi, F.; Song, B.; Liu, C., Toward the Development of the Potential with Angular Distortion for Halogen Bond: A Comparison of Potential Energy Surfaces between Halogen Bond and Hydrogen Bond. The Journal of Physical Chemistry A* 2014, 118 (39), 9140-9147. 15.Wang, L.; Che, X.; Li, H.; Gao, J.; Liu, C., Theoretical study on the working mechanism of a reversible light-driven rotary molecular motor. Theoretical Chemistry Accounts* 2014, 133 (10), 1-8. 16.Shen, L.; Chen, Y.; Li, X.; Gao, J., Effects of Substituents on Tetracene Derivatives on Their Stabilities and Singlet Fission. Journal of Molecular Graphics and Modelling 2014, 51 (0), 86-96. 17.Che, X.; *Gao, J.*; Liu, Y.; Liu, C., Metal vs. chalcogen competition in the catalytic mechanism of cysteine dioxygenase. Journal of Inorganic Biochemistry* 2013, 122 (0), 1-7. 18.Che, X.; *Gao, J.*; Du, L.; Liu, C., Theoretical Investigation of the High-Spin "Fe-Proximal Oxygen" Catalytic Mechanism of Rat Cysteine Dioxygenase. J Theor Comput Chem 2013, 12 (3), 1350001-10. 19.Bi, F.; *Gao, J.*; Wang, L.; Du, L.; Song, B.; Liu, C., Polarization-enhanced bonding process of halogen bond, a theoretical study on F–H/F–X (X;=F,Cl,Br;I) and ammonia. Chemical Physics* 2013, 426 (0), 16-22. 20.Wang, Q.; *Gao^,*J.; Liu, Y.; Liu^,C., Molecular dynamics simulation of the interaction between protein tyrosine phosphatase 1B and aryl diketoacid derivatives. Journal of Molecular Graphics and Modelling 2012, 38 (0), 186-193. 21.Gao, J.; Li^,Z.; Russell, T.; Li, Z., Antibody affinity purification using metallic nickel particles. Journal of Chromatography B* 2012, 895–896 (0), 89-93. 22.Che, X.; *Gao, J.*; Zhang, D.; Liu, C., How Do the Thiolate Ligand and its Relative Position Control the Oxygen Activation in the Cysteine Dioxygenase Model? Journal of Physical Chemistry A 2012, 116, 5510-5517. 23.Gao, J.; Li, Z., Uncover the conserved property underlying sequence-distant and structure-similar proteins. Biopolymers 2010, 93 (4), 340-347. 24.Gao, J.; Li, Z., Comparing four different approaches for the determination of inter-residue interactions provides insight for the structure prediction of helical membrane proteins. Biopolymers 2009, 91 (7), 547-556. 25.Gao, J.; Li, Z., Inter-residue interactions in protein structures exhibit power-law behavior. Biopolymers 2008, 89 (12), 1174-178. 26.Gao, J.; Li, Z., Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone. Journal of Computer-Aided Molecular Design 2008, 23 (11), 755-763. 27.Gao, J.; Zou, W.; Liu, W.; Xiao, Y.; Peng, D.; Song, B.; Liu, C., Time-dependent four-component relativistic density-functional theory for excitation energies. II. The exchange-correlation kernel. Journal of Chemical Physics 2005, 123 (5), 054102 28.Gao, J.; Liu, W.; Song, B.; Liu, C., Time-dependent four-component relativistic density functional theory for excitation energies. Journal of Chemical Physics 2004, 121 (14), 6658.