List of works - Haibo Yu

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis

scientific article published on December 2006

11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules

scientific article published on 19 July 2019

A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide ⬇️

scientific article published on August 11, 2010

A new class of quadruplex DNA-binding nickel Schiff base complexes

scientific article published on 27 March 2020

A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function

scientific article published on 01 September 2018

Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations

scientific article

Ammonium Aminodiboranate: A Long-Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer

scientific article published on 26 April 2016

Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin

scientific article published on 16 December 2019

Biomolecular modeling: Goals, problems, perspectives

scientific article published on June 2006

Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

scientific article published on 15 November 2004

Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC

scientific article published in Scientific Reports

Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study

scientific article

Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design.

scientific article

Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design

scientific article published on 16 December 2015

Computer-aided design of human sialyltransferase inhibitors of hST8Sia III.

scientific article published on 9 November 2017

Depolymerization of sodium polyphosphates on an iron oxide surface at high temperature.

scientific article published on 5 March 2018

Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization

scientific article published on January 2008

Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks.

scientific article published in May 2001

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes

scientific article published in April 2006

Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids.

scientific article published on 2 April 2018

Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus

scientific article published on 23 April 2014

Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones

scientific article published on 09 August 2019

Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

scientific article

Engineering the hERG1 Selectivity Filter into the NaK Pore Domain

Exploration of the Dehydrogenation Pathways of Ammonia Diborane and Diammoniate of Diborane by Molecular Dynamics Simulations Using Reactive Force Fields

scientific article published on 25 February 2020

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

scientific article published on 3 October 2007

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.

scientific article published on July 2008

Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting

scientific article published on 14 December 2018

Hydration number, topological control, and ion selectivity.

scientific article published on June 2009

Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches

scientific article published on 12 January 2015

Ion selectivity in channels and transporters

scientific article

Mechanisms of Pressure-Induced Structural Transformation in Confined Sodium Borate Glasses

scientific article published on 19 December 2019

Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations

scientific article

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues

scientific article

Molecular Docking Studies to Explore Potential Binding Pockets and Inhibitors for Chikungunya Virus Envelope Glycoproteins

scientific article

Molecular Quantum Dot Cellular Automata Based on Diboryl Monoradical Anions

Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability

article

Molecular dynamics simulations of liquid methanol and methanol–water mixtures with polarizable models

article

Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding

scientific article

Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins

article

On the utilization of energy minimization to the study of ion selectivity

scientific article published on October 2009

Polarisable force fields: what do they add in biomolecular simulations?

scientific article published on 07 February 2020

Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump ⬇️

scientific article published on September 11, 2011

Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

scientific article published on 11 September 2019

Rationalising pKa shifts in Bacillus circulans xylanase with computational studies.

scientific article published on 3 August 2016

Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABAA receptors

scientific article published in PLoS ONE

Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B.

scientific article

Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations

scientific article

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

scientific article

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

scientific article published on January 2013

Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom

scientific article published on 25 December 2019

The effect of DNA backbone on the triplet mechanism of UV-induced thymine-thymine (6-4) dimer formation

article

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

article

Theoretical Investigation on the Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis

scientific article published on 25 September 2019

Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation.

scientific article published on 31 October 2017

Two mechanisms of ion selectivity in protein binding sites

scientific article

pKa cycling of the general acid/base in glycoside hydrolase families 33 and 34.

scientific article published on 18 February 2014

List of works by Haibo Yu

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis

11B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules

A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N-Methylacetamide ⬇️

A new class of quadruplex DNA-binding nickel Schiff base complexes

A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function

Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations

Ammonium Aminodiboranate: A Long-Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer

Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin

Biomolecular modeling: Goals, problems, perspectives

Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC

Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study

Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design.

Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design

Computer-aided design of human sialyltransferase inhibitors of hST8Sia III.

Depolymerization of sodium polyphosphates on an iron oxide surface at high temperature.

Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization

Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks.

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes

Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids.

Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus

Divergent Pd-catalyzed cross-coupling of allenyloxazolidinones to give chiral 1,3-dienes and vinyloxazolidinones

Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

Engineering the hERG1 Selectivity Filter into the NaK Pore Domain

Exploration of the Dehydrogenation Pathways of Ammonia Diborane and Diammoniate of Diborane by Molecular Dynamics Simulations Using Reactive Force Fields

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

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin.

Heteroatom-doped MoSe2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting

Hydration number, topological control, and ion selectivity.

Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches

Ion selectivity in channels and transporters

Mechanisms of Pressure-Induced Structural Transformation in Confined Sodium Borate Glasses

Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations

Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues

Molecular Docking Studies to Explore Potential Binding Pockets and Inhibitors for Chikungunya Virus Envelope Glycoproteins

Molecular Quantum Dot Cellular Automata Based on Diboryl Monoradical Anions

Molecular dynamics simulation of human interleukin-4: comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability

Molecular dynamics simulations of liquid methanol and methanol–water mixtures with polarizable models

Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding

Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins

On the utilization of energy minimization to the study of ion selectivity

Polarisable force fields: what do they add in biomolecular simulations?

Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump ⬇️

Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

Rationalising pKa shifts in Bacillus circulans xylanase with computational studies.

Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABAA receptors

Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B.

Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field

Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom

The effect of DNA backbone on the triplet mechanism of UV-induced thymine-thymine (6-4) dimer formation

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

Theoretical Investigation on the Single Transition-Metal Atom-Decorated Defective MoS2 for Electrocatalytic Ammonia Synthesis

Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation.

Two mechanisms of ion selectivity in protein binding sites

pKa cycling of the general acid/base in glycoside hydrolase families 33 and 34.