Yu, Haibo

Overview

Haibo completed his undergraduate study at the University of Science and Technology of China under the supervision of Professor Yunyu Shi and his Ph.D. at the ETH Zürich under the supervision of Professor Wilfred F. van Gunsteren. He then conducted postdoctoral training at the University of Wisconsin-Madison with Professor Qiang Cui and the University of Chicago with Professor Benoît Roux in the United States. He joined the School of Chemistry at the University of Wollongong in July 2010. Currently, he is also an Honorary Research Fellow at IHMRI.

Top Publications

Year	Title
2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design
2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer
2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34
2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump
2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide

Research Areas

Research Overview

The research program in the Yu Research Group covers a broad range of topics in the area of theoretical/computational chemistry and biophysics. The common goal underlying these research directions is to develop effective theoretical and computational models for complex molecular processes in order to gain new physical insights into the mechanism at a quantitative level.

Available as Research Supervisor

Member Of

Centre for Medical and Molecular Bioscience Member 2010 -
School of Chemistry Academic Staff 2010 -
Illawarra Health and Medical Research Institute Honorary Research Fellow 2016 - 2019

Selected Publications

Chapter

Year	Title
2010	Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain Pages 23 - 46

Conference Paper

Year	Title
2013	Virtual screening identifies lupeol as an allosteric inhibitor of PTP1B Pages 122 - 122
2012	Catalysis in silico Pages 176 - 176

Journal Article

Year	Title
2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design Published In Advances in Protein Chemistry and Structural Biology Volume 109 Pages 25 - 76
2017	Molecular docking studies to explore potential binding pockets and inhibitors for chikungunya virus envelope glycoproteins Published In Interdisciplinary Sciences: Computational Life Sciences Volume Online First Pages 1 - 10
2017	Theoretical pKa prediction of the α-phosphate moiety of uridine 5′-diphosphate-GlcNAc Published In Chemical Physics Letters Volume 667 Pages 220 - 225
2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer Published In Chemistry: A European Journal Volume 22 Pages 7727 - 7729
2016	Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design Published In Journal of Molecular Recognition Volume 29 Pages 210 - 222
2016	Rationalising pKa shifts in Bacillus circulans xylanase with computational studies Published In Physical Chemistry Chemical Physics Volume 18 Pages 30305 - 30312
2016	Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B Published In Scientific Reports Volume 6 Pages 20766-1 - 20766-14
2015	Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches Published In Journal of Molecular Graphics and Modelling Volume 57 Pages 1 - 8
2014	Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus Published In Journal of Molecular Modeling Volume 20 Pages 2216-1 - 2216-12
2014	In silico enzyme modelling Published In Australian Biochemist Volume 45 Pages 12 - 15
2014	Oxygen binding sites in obelin: a computational study into the formation of active photoproteins Published In Luminescence: journal of biological and chemical luminescence Volume 29 Pages 21 - 21
2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34 Published In Physical Chemistry Chemical Physics Volume 16 Pages 5785 - 5792
2013	Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations Published In Topics in Current Chemistry Volume 337 Pages 139 - 164
2013	Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field Published In Faraday Discussions Volume 160 Pages 135 - 149
2012	Molecular mechanisms of K+ selectivity in Na/K pump Published In Australian Journal of Chemistry: an international journal for chemical science Volume 65 Pages 448 - 456
2011	Ion selectivity in channels and transporters Published In Journal of General Physiology Volume 137 Pages 415 - 426
2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump Published In Nature Structural and Molecular Biology Volume 18 Pages 1159 - 1163
2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide Published In Journal of the American Chemical Society Volume 132 Pages 10847 - 10856
2010	Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory Published In Journal of Chemical Physics Volume 132 Pages 234101-1 - 234101-13
2010	Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations Published In Proceedings of the National Academy of Sciences of USA Volume 107 Pages 18718 - 18723
2010	Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field Published In Journal of Chemical Theory and Computation Volume 6 Pages 774 - 786
2010	Two mechanisms of ion selectivity in protein binding sites Published In Proceedings of the National Academy of Sciences of USA Volume 107 Pages 20329 - 20334
2009	Hydration number, topological control, and ion selectivity Published In The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter Volume 113 Pages 8725 - 8730
2009	On the utilization of energy minimization to the study of ion selectivity Published In Biophysical Journal Volume 97 Pages L15 - L17
2008	Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin Published In Proceedings of the National Academy of Sciences of USA Volume 105 Pages 19672 - 19677
2008	Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory: 1. Parameterization Published In Journal of Chemical Theory and Computation Volume 4 Pages 2067 - 2084
2008	Extensive conformational transitions are required to turn on ATP hydrolysis in myosin Published In Journal of Molecular Biology Volume 381 Pages 1407 - 1420
2008	Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation Published In Chemical Physics Letters Volume 452 Pages 78 - 83
2007	Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction Published In The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory Volume 111 Pages 10861 - 10873
2007	Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations Published In PLoS Computational Biology Volume 3 Pages 0199 - 0213
2007	Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues Published In PLoS Computational Biology Volume 3 Pages 0214 - 0230
2007	Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability Published In Molecular Simulation Volume 33 Pages 1143 - 1154
2007	The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding Published In Journal of Chemical Physics Volume 127 Pages 234504-1 - 234504-8

Investigator On

Year	Title
2017	Liquid-phase hydrogen carriers for energy storage and delivery Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2014	Renewing Intersect's share of the National Computational Infrastructure's peak facility Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
	missing activity

Available as Research Supervisor

Potential Supervision Topics

- Develop computational and theoretical models to study biomolecular and nanoscale systems
- Computer-aided drug design
- Computational enzymology (combined QM/MM simulations)
- Computer-aided materials design

Advisees

Graduate Advising Relationship

Degree	Research Title	Advisee
Doctor of Philosophy	Modelling of Nanostructures using Continuum Mechanics and Molecular Dynamics Simulations	Dyer, Tom
Doctor of Philosophy	Medicinal Organometallic Chemistry	Gee, Yi Sing
Doctor of Philosophy	Computational Studies on the transfer of O-GlcNAc by O-GlcNAc Transferase (OGLT)	Vipperla, Bhavani Prasad
Doctor of Philosophy	Understanding the Catalytic Mechanisms of Glycoside Hydrolases	Xiao, Kela
Master of Philosophy	Photochemistry of Common Nitrogen Containing Aromatic Heterocycles	Bezzina, James
Doctor of Philosophy	The Rational Design of Selective Inhibitors Targeting Sialyltransferase	Montgomery, Andrew
Doctor of Philosophy	Distonic Radical Reactions of Nitrogen Containing Heterocycles with Simple hydrocarbons	Bright, Cameron
Doctor of Philosophy	Computational Vibrational Spectroscopic Studies of Bioscience systems	Inakollu, Venkatasaisandeep
Doctor of Philosophy	Drug Design and Development Targetting Viruses	Metwaly, Mohamed
Doctor of Philosophy	Quantum modelling of lubricant at interface in metal forming at high temperatures	Ta, Thi Thuy Huong
Doctor of Philosophy	Medicinal Chemistry Studies into 6-Substituted Amiloride Analogues as Inhibitors of the Human and Murine Urokinase Plasminogen Activators	Elsalamouny, Nehad
Doctor of Philosophy	Development of Glycosyltransferase Inhibitors as a Novel Antimetastatic Strategy for Cancer Treatment	Dobie, Christopher
Doctor of Philosophy	Molecular Dynamics Simulation of Novel Ionic Liquids for Potential Applications for Hydrogen Storage	Gao, Peng
Doctor of Philosophy	Understanding the Bioluminescence Mechanism of Marine Luciferases	Griffiths, Thomas

Organizer Of Event

MM2015 - the annual conference of the Association of Molecular Modellers of Australasia 2015

Professional Service Activities

Scientific Reports Editorial Board Member 2014 -
Journal of Molecular Modeling Associate Editor 2012 -

Education And Training

Ph.D., ETH Zurich, Department of Chemistry and Applied Biosciences 2000 - 2004
B.Sc., University of Science and Technology of China, School of Life Sciences 1995 - 2000
University of Chicago, USA, Department of Biochemistry and Molecular Biology 2007 - 2010
University of Wisconsin - Madison, USA, Department of Chemistry 2005 - 2007

Awards And Honors

Future Fellowship, conferred by Australian Research Council (ARC), 2012 - 2016

Keywords

Biomolecular simulations, free energy calculations, combined QM/MM simulations, computational biophysics, computer-aided drug design, computer-aided materials design

Full Name

Haibo Yu

Mailing Address

School of Chemistry

University of Wollongong

Wollongong

NSW

2500

Australia

Located In Facility

Building 18 Room G26

Orcid Id

http://orcid.org/0000-0002-1099-2803 (confirmed)

Web Of Science Researcher Id

B-9750-2008

Top Publications

Year	Title
2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design
2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer
2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34
2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump
2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide

Research Areas

Research Overview

The research program in the Yu Research Group covers a broad range of topics in the area of theoretical/computational chemistry and biophysics. The common goal underlying these research directions is to develop effective theoretical and computational models for complex molecular processes in order to gain new physical insights into the mechanism at a quantitative level.

Member Of

Centre for Medical and Molecular Bioscience Member 2010 -
School of Chemistry Academic Staff 2010 -
Illawarra Health and Medical Research Institute Honorary Research Fellow 2016 - 2019

Selected Publications

Chapter

Year	Title
2010	Mechanochemical coupling in molecular motors: insights from molecular simulations of the myosin motor domain Pages 23 - 46

Conference Paper

Year	Title
2013	Virtual screening identifies lupeol as an allosteric inhibitor of PTP1B Pages 122 - 122
2012	Catalysis in silico Pages 176 - 176

Journal Article

Year	Title
2017	Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design Published In Advances in Protein Chemistry and Structural Biology Volume 109 Pages 25 - 76
2017	Molecular docking studies to explore potential binding pockets and inhibitors for chikungunya virus envelope glycoproteins Published In Interdisciplinary Sciences: Computational Life Sciences Volume Online First Pages 1 - 10
2017	Theoretical pKa prediction of the α-phosphate moiety of uridine 5′-diphosphate-GlcNAc Published In Chemical Physics Letters Volume 667 Pages 220 - 225
2016	Ammonium aminodiboranate: A long-sought isomer of diammoniate of diborane and ammonia borane dimer Published In Chemistry: A European Journal Volume 22 Pages 7727 - 7729
2016	Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design Published In Journal of Molecular Recognition Volume 29 Pages 210 - 222
2016	Rationalising pKa shifts in Bacillus circulans xylanase with computational studies Published In Physical Chemistry Chemical Physics Volume 18 Pages 30305 - 30312
2016	Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B Published In Scientific Reports Volume 6 Pages 20766-1 - 20766-14
2015	Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches Published In Journal of Molecular Graphics and Modelling Volume 57 Pages 1 - 8
2014	Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus Published In Journal of Molecular Modeling Volume 20 Pages 2216-1 - 2216-12
2014	In silico enzyme modelling Published In Australian Biochemist Volume 45 Pages 12 - 15
2014	Oxygen binding sites in obelin: a computational study into the formation of active photoproteins Published In Luminescence: journal of biological and chemical luminescence Volume 29 Pages 21 - 21
2014	PKa cycling of the general acid/base in glycoside hydrolase families 33 and 34 Published In Physical Chemistry Chemical Physics Volume 16 Pages 5785 - 5792
2013	Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations Published In Topics in Current Chemistry Volume 337 Pages 139 - 164
2013	Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field Published In Faraday Discussions Volume 160 Pages 135 - 149
2012	Molecular mechanisms of K+ selectivity in Na/K pump Published In Australian Journal of Chemistry: an international journal for chemical science Volume 65 Pages 448 - 456
2011	Ion selectivity in channels and transporters Published In Journal of General Physiology Volume 137 Pages 415 - 426
2011	Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump Published In Nature Structural and Molecular Biology Volume 18 Pages 1159 - 1163
2010	A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide Published In Journal of the American Chemical Society Volume 132 Pages 10847 - 10856
2010	Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory Published In Journal of Chemical Physics Volume 132 Pages 234101-1 - 234101-13
2010	Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations Published In Proceedings of the National Academy of Sciences of USA Volume 107 Pages 18718 - 18723
2010	Simulating monovalent and divalent ions in aqueous solution using a drude polarizable force field Published In Journal of Chemical Theory and Computation Volume 6 Pages 774 - 786
2010	Two mechanisms of ion selectivity in protein binding sites Published In Proceedings of the National Academy of Sciences of USA Volume 107 Pages 20329 - 20334
2009	Hydration number, topological control, and ion selectivity Published In The Journal of Physical Chemistry B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter Volume 113 Pages 8725 - 8730
2009	On the utilization of energy minimization to the study of ion selectivity Published In Biophysical Journal Volume 97 Pages L15 - L17
2008	Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin Published In Proceedings of the National Academy of Sciences of USA Volume 105 Pages 19672 - 19677
2008	Description of phosphate hydrolysis reactions with the self-consistent-charge density-functional-tight-binding (SCC-DFTB) theory: 1. Parameterization Published In Journal of Chemical Theory and Computation Volume 4 Pages 2067 - 2084
2008	Extensive conformational transitions are required to turn on ATP hydrolysis in myosin Published In Journal of Molecular Biology Volume 381 Pages 1407 - 1420
2008	Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation Published In Chemical Physics Letters Volume 452 Pages 78 - 83
2007	Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction Published In The Journal of Physical Chemistry A: Isolated Molecules, Clusters, Radicals, and Ions; Environmental Chemistry, Geochemistry, and Astrochemistry; Theory Volume 111 Pages 10861 - 10873
2007	Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations Published In PLoS Computational Biology Volume 3 Pages 0199 - 0213
2007	Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues Published In PLoS Computational Biology Volume 3 Pages 0214 - 0230
2007	Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability Published In Molecular Simulation Volume 33 Pages 1143 - 1154
2007	The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding Published In Journal of Chemical Physics Volume 127 Pages 234504-1 - 234504-8

Investigator On

Year	Title
2017	Liquid-phase hydrogen carriers for energy storage and delivery Awarded by: Australian Research Council (ARC) Funding Scheme: Discovery Projects
2014	Renewing Intersect's share of the National Computational Infrastructure's peak facility Awarded by: Australian Research Council (ARC) Funding Scheme: Linkage Infrastructure Equipment & Facilities (LIEF)
	missing activity

Potential Supervision Topics

- Develop computational and theoretical models to study biomolecular and nanoscale systems
- Computer-aided drug design
- Computational enzymology (combined QM/MM simulations)
- Computer-aided materials design

Advisees

Graduate Advising Relationship

Degree	Research Title	Advisee
Doctor of Philosophy	Modelling of Nanostructures using Continuum Mechanics and Molecular Dynamics Simulations	Dyer, Tom
Doctor of Philosophy	Medicinal Organometallic Chemistry	Gee, Yi Sing
Doctor of Philosophy	Computational Studies on the transfer of O-GlcNAc by O-GlcNAc Transferase (OGLT)	Vipperla, Bhavani Prasad
Doctor of Philosophy	Understanding the Catalytic Mechanisms of Glycoside Hydrolases	Xiao, Kela
Master of Philosophy	Photochemistry of Common Nitrogen Containing Aromatic Heterocycles	Bezzina, James
Doctor of Philosophy	The Rational Design of Selective Inhibitors Targeting Sialyltransferase	Montgomery, Andrew
Doctor of Philosophy	Distonic Radical Reactions of Nitrogen Containing Heterocycles with Simple hydrocarbons	Bright, Cameron
Doctor of Philosophy	Computational Vibrational Spectroscopic Studies of Bioscience systems	Inakollu, Venkatasaisandeep
Doctor of Philosophy	Drug Design and Development Targetting Viruses	Metwaly, Mohamed
Doctor of Philosophy	Quantum modelling of lubricant at interface in metal forming at high temperatures	Ta, Thi Thuy Huong
Doctor of Philosophy	Medicinal Chemistry Studies into 6-Substituted Amiloride Analogues as Inhibitors of the Human and Murine Urokinase Plasminogen Activators	Elsalamouny, Nehad
Doctor of Philosophy	Development of Glycosyltransferase Inhibitors as a Novel Antimetastatic Strategy for Cancer Treatment	Dobie, Christopher
Doctor of Philosophy	Molecular Dynamics Simulation of Novel Ionic Liquids for Potential Applications for Hydrogen Storage	Gao, Peng
Doctor of Philosophy	Understanding the Bioluminescence Mechanism of Marine Luciferases	Griffiths, Thomas

Organizer Of Event

MM2015 - the annual conference of the Association of Molecular Modellers of Australasia 2015

Professional Service Activities

Scientific Reports Editorial Board Member 2014 -
Journal of Molecular Modeling Associate Editor 2012 -

Education And Training

Ph.D., ETH Zurich, Department of Chemistry and Applied Biosciences 2000 - 2004
B.Sc., University of Science and Technology of China, School of Life Sciences 1995 - 2000
University of Chicago, USA, Department of Biochemistry and Molecular Biology 2007 - 2010
University of Wisconsin - Madison, USA, Department of Chemistry 2005 - 2007

Awards And Honors

Future Fellowship, conferred by Australian Research Council (ARC), 2012 - 2016

Keywords

Biomolecular simulations, free energy calculations, combined QM/MM simulations, computational biophysics, computer-aided drug design, computer-aided materials design

Full Name

Haibo Yu

Mailing Address

School of Chemistry

University of Wollongong

Wollongong

NSW

2500

Australia

Located In Facility

Building 18 Room G26

Orcid Id

http://orcid.org/0000-0002-1099-2803 (confirmed)

Web Of Science Researcher Id

B-9750-2008

Overview

Overview

Top Publications

Research Areas

Research Overview

Available as Research Supervisor

Affiliation

Member Of

Publications

Selected Publications

Chapter

Conference Paper

Journal Article

Funding

Investigator On

Supervision

Available as Research Supervisor

Potential Supervision Topics

Advisees

Graduate Advising Relationship

Service

Organizer Of Event

Professional Service Activities

Background

Education And Training

Awards And Honors

Keywords

Contact

Full Name

Mailing Address

Located In Facility

Identity

Orcid Id

Web Of Science Researcher Id

Overview

Top Publications

Research Areas

Research Overview

Affiliation

Member Of

Publications

Selected Publications

Chapter

Conference Paper

Journal Article

Funding

Investigator On

Supervision

Potential Supervision Topics

Advisees

Graduate Advising Relationship

Service

Organizer Of Event

Professional Service Activities

Background

Education And Training

Awards And Honors

Keywords

Contact

Full Name

Mailing Address

Located In Facility

Identity

Orcid Id

Web Of Science Researcher Id

Visualisations

Research Areas