Papers

For the most up-to-date list, see .

Preprints & Data Peer-reviewed Articles

Preprints & Data

This is an incomplete list. Most preprints have been submitted to a journal for publications.

  1. Modulation of Adenosine Diphosphate-Magnesium Ion Radical Pair Spin Populations in an External Magnetic Field
    Manian, Anjay and Paz, Holden and Raza, Zahra and Yu, Haibo
    2026
  2. Vibronic Contributions to Hyperfine-Mediated Spin Kinetics
    Manian, Anjay and Paz, Holden and Yu, Haibo
    2025
  3. Mechanistic Insights into Nanobody-Based Quenchbody Sensing via Structural Modeling and Molecular Simulations
    El Salamouni, Nehad and Cater, Jordan and Zhu, Qiang and Spenkelink, Lisanne and Yu, Haibo
    2025
  4. DNA Barcoding for Parallelised Single-Molecule Characterisation of Kinetic Phenotypes
    Mueller, Stefan H. and Grimson, David M. and Paz, Holden and Fitch, Aidan C. and Yu, Haibo and Ribezzi-Crivellari, Marco and Griffiths, Andrew D. and Van Oijen, Antoine M and Spenkelink, Lisanne M.
    2025
  5. EBV BALF2 DNA Annealing Intermediate Structure Reveals the Mechanism of Annealing during Recombination
    Tolun, Gökhan and Nicholls, Jordan and Brewster, Jodi and Salamouni, Nehad El and Johnston, Nikolas and Yu, Haibo
    2025
  6. Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches
    Zhu, Qiang and Raza, Zahra and Do-Ha, Dzung and De Costa, Emma and Sasheva, Pavlina and McAlary, Luke and Mahmodi, Hadi and Bowen, Warwick and Ooi, Lezanne and Kabakova, Irina and Yu, Haibo
    2025
  7. Active Site Plasticity of the Bacterial Sliding Clamp
    Raza, Zahra and El Salamouni, Nehad and McElroy, Andrew and Skropeta, Danielle and Kelso, Michael and Oakley, Aaron and Dixon, Nicholas and Yu, Haibo
    2024
  8. Nanobody Engineering: Computational Modelling and Design for Biomedical and Therapeutic Applications
    El Salamouni, Nehad and Cater, Jordan and Spenkelink, Lisanne and Yu, Haibo
    2024
  9. Optimised Nanobody-Based Quenchbodies for Enhanced Protein Detection
    Cater, Jordan Harry and Elsalamouny, Nehad and Mansour, Ghada H and Hutchinson, Sebastian and Mc Guinness, Conall and Mueller, Stefan H. and Spinks, Richard Raymond and Shanmugam, Nirukshan and Pichard-Kostuch, Adeline and Zahoransky, Viktor and Ghodke, Harshad and Ribezzi-Crivellari, Marco and Yu, Haibo and Van Oijen, Antoine M and Griffiths, Andrew D. and Spenkelink, Lisanne M.
    2024
  10. Ion Transport and Inhibitor Binding by Human NHE1: Insights from Molecular Dynamics Simulations and Free Energy Calculations
    El Salamouni, Nehad and Buckley, Benjamin and Lee, Richmond and Ranson, Marie and Kelso, Michael and Yu, Haibo
  11. Predicting Solvent Effects on SN2 Reaction Rates – Comparison of QM/MM, Implicit and MM Explicit Solvent Models
    Taylor, Mackenzie and Yu, Haibo and Ho, Junming
    2022
  12. Structure of Phage λ Redβ\textsubscript177 Annealase Shows How It Anneals DNA Strands during Single-Strand Annealing Homologous DNA Recombination
    Newing, Timothy and Brewster, Jodi L. and Yu, Haibo and Johnston, Nikolas P. and Fitschen, Lucy J. and Tolun, Gökhan
    2022
  13. Direct SN2 or SN2X Manifold – Mechanistic Study of Ion-Pair Catalyzed Carbon(Sp3)-Carbon(Sp3) Bond Formation
    Lee, Richmond and Chao, Chi Bong Eric and Ban, Xu and Tan, Siu Min and Yu, Haibo and Hyland, Christopher J. T. and Tan, Choon-Hong
    2021
  14. Disruption of Water Networks Is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA)
    El Salamouni, Nehad and Buckley, Benjamin and Jiang, Longguang and Huang, Mingdong and Ranson, Marie and Kelso, Michael and Yu, Haibo
    2021
  15. Comparative Studies of IR Spectra of Deprotonated Serine with Classical and Thermostated Ring Polymer Molecular Dynamics Simulations
    Inakollu, V. S. Sandeep and Yu, Haibo
    2021
  16. Urokinase Plasminogen Activator as an Anti-Metastasis Target: Inhibitor Design Principles, Recent Amiloride Derivatives and Issues with Human/Mouse Species Selectivity
    Salamouni, Nehad S El and Buckley, Benjamin J and Ranson, Marie and Kelso, Michael J and Yu, Haibo
  17. Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols
    Awoonor-Williams, Ernest and Isley, William and Dale, Stephen and Johnson, Erin and Yu, Haibo and Becke, Axel and Roux, Benoît and Rowley, Christopher
    2019

Peer-reviewed Articles (2010–)

  1. Mechanistic Insights into Nanobody-Based Quenchbody Sensing via Structural Modeling and Molecular Simulations
    El Salamouni, Nehad S. and Cater, Jordan H. and Zhu, Qiang and Spenkelink, Lisanne M. and Yu, Haibo
    Journal of Chemical Information and Modeling :acs.jcim.5c02969, 2026
  2. Tailored Magnetic ZIF-67-derived FeCo-LDH for PETase Immobilization toward Effective Removal and Biodegradation of High-Crystallinity Micro- and Nano-PET
    Chen, Yaxin and Xu, Yixiang and Zhou, Yanhong and Deng, Zhou and Feng, Yu and Zhang, Ruifang and Yang, Chun and Li, Hongchun and Yu, Haibo and Zhang, Guangya
    Journal of Hazardous Materials 500 :140419, 2025
  3. Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches
    Zhu, Qiang and Raza, Zahra and Do-Ha, Dzung and De Costa, Emma and Sasheva, Pavlina and McAlary, Luke and Mahmodi, Hadi and Bowen, Warwick P. and Ooi, Lezanne and Kabakova, Irina and Yu, Haibo
    Advanced Materials 37 (36) :e10115, 2025
  4. Optimised Nanobody-Based Quenchbodies for Enhanced Protein Detection
    Cater, Jordan H. and El Salamouni, Nehad S. and Mansour, Ghada H. and Hutchinson, Sebastian and Mc Guinness, Conall and Mueller, Stefan H. and Spinks, Richard R. and Shanmugam, Nirukshan and Pichard-Kostuch, Adeline and Zahoransky, Viktor and Ghodke, Harshad and Ribezzi-Crivellari, Marco and Yu, Haibo and Van Oijen, Antoine M. and Griffiths, Andrew D. and Spenkelink, Lisanne M.
    Communications Biology 8 (1) :937–947, 2025
  5. The Effects of Conformational Sampling and QM Region Size in QM / MM Simulations: An Adaptive QM / MM Study with Model Systems
    Paz, Holden and Beck, Silvan and Lee, Richmond and Ho, Junming and Yu, Haibo
    Journal of Computational Chemistry 46 (11) :e70109, 2025
  6. Active Site Plasticity of the Bacterial Sliding Clamp
    Raza, Zahra and El Salamouni, Nehad S. and McElroy, Andrew B. and Skropeta, Danielle and Kelso, Michael J. and Oakley, Aaron J. and Dixon, Nicholas E. and Yu, Haibo
    Biochemistry 64 (8) :1762–1769, 2025
  7. Nanobody Engineering: Computational Modelling and Design for Biomedical and Therapeutic Applications
    El Salamouni, Nehad S. and Cater, Jordan H. and Spenkelink, Lisanne M. and Yu, Haibo
    FEBS Open Bio 15 (2) :236–253, 2025
  8. How Accurate Are QM/MM Models?
    Ho, Junming and Yu, Haibo and Shao, Yihan and Taylor, Mackenzie and Chen, Junbo
    The Journal of Physical Chemistry a 129 (6) :1517–1528, 2025
  9. Synthesis of α-Hydroxy-1,2,3-Triazole-Linked Sialyltransferase Inhibitors and Evaluation of Selectivity towards ST3GAL1, ST6GAL1 and ST8SIA2
    Szabo, Rémi and Dobie, Chris and Montgomery, Andrew P. and Steele, Harrison and Yu, Haibo and Skropeta, Danielle
    ChemMedChem 19 (16) :e202400088, 2024
  10. Ion Transport and Inhibitor Binding by Human NHE1: Insights from Molecular Dynamics Simulations and Free Energy Calculations
    El Salamouni, Nehad S. and Buckley, Benjamin J. and Lee, Richmond and Ranson, Marie and Kelso, Michael J. and Yu, Haibo
    The Journal of Physical Chemistry B 128 (2) :441–450, 2024
  11. Design, Synthesis, and Evaluation of Cephamycin-Based Antisporulation Agents Targeting Clostridioides Difficile
    Cun, Wendy Y. and Bate, Clara E. and Srikhanta, Yogitha N. and Hutton, Melanie L. and Webb, Chaille T. and Revitt-Mills, Sarah A. and Lyras, Dena and McGowan, Sheena and Yu, Haibo and Keller, Paul A. and Pyne, Stephen G.
    Journal of Medicinal Chemistry 67 (1) :451–466, 2024
  12. Effect of Substituents on the Ability of Nickel Schiff Base Complexes with Four Pendant Groups to Bind to G-quadruplexes
    Assadawi, Nawal and Ferderer, Myles and Kusi-Appauh, Nicholas and Yu, Haibo and Dillon, Carolyn T. and Sluyter, Ronald and Richardson, Christopher and Ralph, Stephen F.
    Dalton Transactions 53 (30) :12721–12739, 2024
  13. Guanidine-Based Biomimetic Hydrides for Carbon Dioxide Reduction
    Chen, Junbo and Yu, Haibo and Tan, Davin and Lee, Richmond
    Chemical Communications 59 (35) :5201–5204, 2023
  14. Predicting Solvent Effects on S\textsubscriptN 2 Reaction Rates: Comparison of QM/MM, Implicit, and MM Explicit Solvent Models
    Taylor, Mackenzie and Yu, Haibo and Ho, Junming
    The Journal of Physical Chemistry B 126 (44) :9047–9058, 2022
  15. Hydrogen Bonding Penalty Used for Virtual Screening to Discover Potent Inhibitors for Papain-like Cysteine Proteases of SARS-CoV-2
    Zhao, Guangjian and Liu, Xiaochun and Wang, Suyun and Bai, Zhongyue and Zhang, Siyu and Wang, Yifan and Yu, Haibo and Xu, Ximing
    Chemical Biology & Drug Design 100 (4) :502–514, 2022
  16. Redβ177 Annealase Structure Reveals Details of Oligomerization and λ Red-Mediated Homologous DNA Recombination
    Newing, Timothy P. and Brewster, Jodi L. and Fitschen, Lucy J. and Bouwer, James C. and Johnston, Nikolas P. and Yu, Haibo and Tolun, Gökhan
    Nature Communications 13 (1) :5649, 2022
  17. 1,6;2,3-Bis-BN Cyclohexane: Synthesis, Structure, and Hydrogen Release
    Dai, Yan and Zhang, Xin and Liu, Yongfeng and Yu, Haibo and Su, Wei and Zhou, John and Ye, Qing and Huang, Zhenguo
    Journal of the American Chemical Society 144 (19) :8434–8438, 2022
  18. Direct S\textsubscriptN 2 or S\textsubscriptN 2X Manifold-mechanistic Study of Ion-Pair-Catalyzed Carbon(Sp3 )–Carbon(Sp3 ) Bond Formation
    Lee, Richmond and Eric Chao, Chi Bong and Ban, Xu and Tan, Siu Min and Yu, Haibo and Hyland, Christopher J. T. and Tan, Choon-Hong
    The Journal of Organic Chemistry 87 (6) :4029–4039, 2022
  19. Urokinase Plasminogen Activator as an Anti-Metastasis Target: Inhibitor Design Principles, Recent Amiloride Derivatives, and Issues with Human/Mouse Species Selectivity
    El Salamouni, Nehad S and Buckley, Benjamin J. and Ranson, Marie and Kelso, Michael J. and Yu, Haibo
    Biophysical Reviews 14 (1) :277–301, 2022
  20. Disruption of Water Networks Is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA)
    S El Salamouni, Nehad and Buckley, Benjamin J. and Jiang, Longguang and Huang, Mingdong and Ranson, Marie and Kelso, Michael J. and Yu, Haibo
    Journal of Medicinal Chemistry 65 (3) :1933–1945, 2022
  21. Coupling Partner-Dependent Unsymmetrical C–H Functionalization of N -Phenoxyacetamides Leading to Sophisticated Spirocyclic Scaffolds
    Song, Xia and Wang, Kelin and Xue, Lian and Yu, Haibo and Zhang, Xinying and Lee, Richmond and Fan, Xuesen
    Organic Chemistry Frontiers 9 (17) :4583–4590, 2022
  22. Sialyltransferase Inhibitors as Potential Anti-Cancer Agents*
    Skropeta, Danielle and Dobie, Christopher and Montgomery, Andrew P. and Steele, Harrison and Szabo, Rémi and Yu, Haibo
    Australian Journal of Chemistry 74 (11) :758–766, 2021
  23. Comparative Studies of IR Spectra of Deprotonated Serine with Classical and Thermostated Ring Polymer Molecular Dynamics Simulations
    Inakollu, V. S. Sandeep and Yu, Haibo
    Structural Dynamics 8 (5) :54101, 2021
  24. Computational Tribochemistry: A Review from Classical and Quantum Mechanics Studies
    Ta, Huong T. T. and Tran, Nam V. and Tieu, A. Kiet and Zhu, Hongtao and Yu, Haibo and Ta, Thi D.
    The Journal of Physical Chemistry C 125 (31) :16875–16891, 2021
  25. The Detosylation of Chiral 1,2-Bis(Tosylamides)
    Gaston, Jayden J. and Tague, Andrew J. and Smyth, Jamie E. and Butler, Nicholas M. and Willis, Anthony C. and Van Eikema Hommes, Nico and Yu, Haibo and Clark, Timothy and Keller, Paul A.
    The Journal of Organic Chemistry 86 (13) :9163–9180, 2021
  26. An Amine–Borane System Featuring Room-Temperature Dehydrogenation and Regeneration
    Zhang, Guojin and Morrison, Daniel and Bao, Guochen and Yu, Haibo and Yoon, Chang Won and Song, Taekyong and Lee, Jihye and Ung, Alison T. and Huang, Zhenguo
    Angewandte Chemie International Edition 60 (21) :11725–11729, 2021
  27. Postsynthetic Modification of Half-Sandwich Ruthenium Complexes by Mechanochemical Synthesis
    Jia, Wei-Guo and Zhi, Xue-Ting and Li, Xiao-Dong and Zhou, Jun-Peng and Zhong, Rui and Yu, Haibo and Lee, Richmond
    Inorganic Chemistry 60 (7) :4313–4321, 2021
  28. A First-Principles Study of Impurity-Enhanced Adhesion and Lubricity of Graphene on Iron Oxide Surface
    Ta, Huong T. T. and Tieu, A. Kiet and Zhu, Hongtao and Yu, Haibo and Tran, Nam V.
    The Journal of Physical Chemistry C 125 (7) :4311–4321, 2021
  29. Synthesis and Biological Evaluation of Selective Phosphonate-Bearing 1,2,3-Triazole-Linked Sialyltransferase Inhibitors
    Dobie, Christopher and Montgomery, Andrew P. and Szabo, Rémi and Yu, Haibo and Skropeta, Danielle
    RSC Medicinal Chemistry 12 (10) :1681–1689, 2021
  30. Structural Response of Alkali Metal Borates at Fe2O3 Sliding Interface: The Effect of Alkali Cations
    Ta, Huong T.T. and Tieu, A. Kiet and Zhu, Hongtao and Yu, Haibo and Tran, Nam V. and Le, Ha M. and Ta, Thi D.
    Computational Materials Science 184 :109930, 2020
  31. Predicting Phosphirane Air Stability Using Density Functional Theory
    Gaston, Jayden J. and McCosker, Patrick M. and Yu, Haibo and Keller, Paul A.
    Journal of Physical Organic Chemistry 33 (10) :e4110, 2020
  32. Surface Transformation and Interactions of Iron Oxide in Glassy Lubricant: An Ab Initio Study
    Le, M.H. and Tieu, A.K. and Zhu, H. and Ta, D.T. and Yu, H. and Ta, T.T.H. and Tran, V.N.
    Chemical Physics 538 :110919, 2020
  33. Design, Synthesis and Evaluation of Carbamate-Linked Uridyl-Based Inhibitors of Human ST6Gal I
    Montgomery, Andrew P. and Dobie, Christopher and Szabo, Rémi and Hallam, Laura and Ranson, Marie and Yu, Haibo and Skropeta, Danielle
    Bioorganic & Medicinal Chemistry 28 (14) :115561, 2020
  34. Enhanced Potassium Ion Battery by Inducing Interlayer Anionic Ligands in MoS\textsubscript1.5 Se\textsubscript0.5 Nanosheets with Exploration of the Mechanism
    Fan, Hai-Ning and Wang, Xing-Yong and Yu, Hai-Bo and Gu, Qin-Fen and Chen, Shan-Liang and Liu, Zheng and Chen, Xiao-Hua and Luo, Wen-Bin and Liu, Hua-Kun
    Advanced Energy Materials 10 (21) :1904162, 2020
  35. Structural Basis of the Potency and Selectivity of Urotoxin, a Potent Kv1 Blocker from Scorpion Venom
    Luna-Ramirez, Karen and Csoti, Agota and McArthur, Jeffrey R. and Chin, Yanni K.Y. and Anangi, Raveendra and Najera, Rosby Del Carmen and Possani, Lourival D. and King, Glenn F. and Panyi, Gyorgy and Yu, Haibo and Adams, David J. and Finol-Urdaneta, Rocio K.
    Biochemical Pharmacology 174 :113782, 2020
  36. Polarisable Force Fields: What Do They Add in Biomolecular Simulations?
    Inakollu, Vs Sandeep and Geerke, Daan P and Rowley, Christopher N and Yu, Haibo
    Current Opinion in Structural Biology 61 :182–190, 2020
  37. Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin
    Griffiths, Thomas M. and Oakley, Aaron J. and Yu, Haibo
    Journal of Computational Chemistry 41 (6) :587–603, 2020
  38. Exploration of the Dehydrogenation Pathways of Ammonia Diborane and Diammoniate of Diborane by Molecular Dynamics Simulations Using Reactive Force Fields
    Gao, Peng and Huang, Zhenguo and Yu, Haibo
    The Journal of Physical Chemistry a 124 (9) :1698–1704, 2020
  39. Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols
    Awoonor-Williams, Ernest and Isley, William C. and Dale, Stephen G. and Johnson, Erin R. and Yu, Haibo and Becke, Axel D. and Roux, Benoît and Rowley, Christopher N.
    Journal of Computational Chemistry 41 (5) :427–438, 2020
  40. Ab Initio Study on Physical and Chemical Interactions at Borates and Iron Oxide Interface at High Temperature
    Ta, Huong T.T. and Tieu, A. Kiet and Zhu, Hongtao and Yu, Haibo and Tran, Nam V. and Tran, Bach H. and Wan, Shanhong and Ta, Thi D.
    Chemical Physics 529 :110548, 2020
  41. Mechanisms of Pressure-Induced Structural Transformation in Confined Sodium Borate Glasses
    Ta, Huong T. T. and Tieu, A. Kiet and Zhu, Hongtao and Yu, Haibo and Tran, Nam V. and Ta, Thi D.
    The Journal of Physical Chemistry B 124 (1) :277–287, 2020
  42. A New Class of Quadruplex DNA-binding Nickel Schiff Base Complexes
    Pham, Son Q. T. and Assadawi, Nawal and Wells, Jadon and Sophocleous, Reece A. and Davis, Kimberley J. and Yu, Haibo and Sluyter, Ronald and Dillon, Carolyn T. and Kelso, Celine and Beck, Jennifer L. and Willis, Anthony C. and Richardson, Christopher and Ralph, Stephen F.
    Dalton Transactions 49 (15) :4843–4860, 2020
  43. Theoretical Screening of Single Transition Metal Atoms Embedded in MXene Defects as Superior Electrocatalyst of Nitrogen Reduction Reaction
    Li, Lei and Wang, Xingyong and Guo, Haoran and Yao, Ge and Yu, Haibo and Tian, Ziqi and Li, Baihai and Chen, Liang
    Small Methods 3 (11) :1900337, 2019
  44. Theoretical Investigation on the Single Transition-Metal Atom-Decorated Defective MoS\textsubscript2 for Electrocatalytic Ammonia Synthesis
    Guo, Haoran and Li, Lei and Wang, Xingyong and Yao, Ge and Yu, Haibo and Tian, Ziqi and Li, Baihai and Chen, Liang
    ACS Applied Materials & Interfaces 11 (40) :36506–36514, 2019
  45. Electrocatalytically Inactive SnS2 Promotes Water Adsorption/Dissociation on Molybdenum Dichalcogenides for Accelerated Alkaline Hydrogen Evolution
    Chen, Yaping and Wang, Xingyong and Lao, Mengmeng and Rui, Kun and Zheng, Xiaobo and Yu, Haibo and Ma, Jing and Dou, Shi Xue and Sun, Wenping
    Nano Energy 64 :103918, 2019
  46. 11 B NMR Chemical Shift Predictions via Density Functional Theory and Gauge-Including Atomic Orbital Approach: Applications to Structural Elucidations of Boron-Containing Molecules
    Gao, Peng and Wang, Xingyong and Huang, Zhenguo and Yu, Haibo
    ACS Omega 4 (7) :12385–12392, 2019
  47. Towards an Accurate Prediction of Nitrogen Chemical Shifts by Density Functional Theory and Gauge-Including Atomic Orbital
    Gao, Peng and Wang, Xingyong and Yu, Haibo
    Advanced Theory and Simulations 2 (2) :1800148, 2019
  48. Comparative Studies of Catalytic Pathways for Streptococcus Pneumoniae Sialidases NanA, NanB and NanC
    Xiao, Kela and Wang, Xingyong and Yu, Haibo
    Scientific Reports 9 (1) :2157, 2019
  49. Heteroatom-Doped MoSe\textsubscript2 Nanosheets with Enhanced Hydrogen Evolution Kinetics for Alkaline Water Splitting
    Zhao, Guoqiang and Wang, Xingyong and Wang, Shaolan and Rui, Kun and Chen, Yaping and Yu, Haibo and Ma, Jing and Dou, Shi Xue and Sun, Wenping
    Chemistry – an Asian Journal 14 (2) :301–306, 2019
  50. Divergent Pd-Catalyzed Cross-Coupling of Allenyloxazolidinones to Give Chiral 1,3-Dienes and Vinyloxazolidinones
    Brown, Ronald W. and Zamani, Farzad and Gardiner, Michael G. and Yu, Haibo and Pyne, Stephen G. and Hyland, Christopher J. T.
    Chemical Science 10 (39) :9051–9056, 2019
  51. Remodeling the Endoplasmic Reticulum Proteostasis Network Restores Proteostasis of Pathogenic GABAA Receptors
    Fu, Yan-Lin and Han, Dong-Yun and Wang, Ya-Juan and Di, Xiao-Jing and Yu, Hai-Bo and Mu, Ting-Wei
    PLOS One 13 (11) :e0207948, 2018
  52. The Effect of DNA Backbone on the Triplet Mechanism of UV-induced Thymine-Thymine (6–4) Dimer Formation
    Wang, Xingyong and Yu, Haibo
    Journal of Molecular Modeling 24 (11) :319–327, 2018
  53. A Systematic Benchmarking of Computational Vibrational Spectroscopy with DFTB3: Normal Mode Analysis and Fast Fourier Transform Dipole Autocorrelation Function
    Inakollu, V. S. Sandeep and Yu, Haibo
    Journal of Computational Chemistry 39 (25) :2067–2078, 2018
  54. Molecular Docking Studies to Explore Potential Binding Pockets and Inhibitors for Chikungunya Virus Envelope Glycoproteins
    Nguyen, Phuong T. V. and Yu, Haibo and Keller, Paul A.
    Interdisciplinary Sciences: Computational LIFE Sciences 10 (3) :515–524, 2018
  55. Differential-Mobility Spectrometry of 1-Deoxysphingosine Isomers: New Insights into the Gas Phase Structures of Ionized Lipids
    Poad, Berwyck L. J. and Maccarone, Alan T. and Yu, Haibo and Mitchell, Todd W. and Saied, Essa M. and Arenz, Christoph and Hornemann, Thorsten and Bull, James N. and Bieske, Evan J. and Blanksby, Stephen J.
    Analytical Chemistry 90 (8) :5343–5351, 2018
  56. Computer-Aided Design of Human Sialyltransferase Inhibitors of hST8Sia III
    Dobie, Christopher and Montgomery, Andrew P. and Szabo, Rémi and Skropeta, Danielle and Yu, Haibo
    Journal of Molecular Recognition 31 (2) :e2684, 2018
  57. Molecular Quantum Dot Cellular Automata Based on Diboryl Monoradical Anions
    Wang, Xingyong and Yu, Lirong and Inakollu, V. S. Sandeep and Pan, Xiaobo and Ma, Jing and Yu, Haibo
    The Journal of Physical Chemistry C 122 (4) :2454–2460, 2018
  58. Depolymerization of Sodium Polyphosphates on an Iron Oxide Surface at High Temperature
    Le, M. H. and Tieu, A. K. and Zhu, H. and Ta, D. T. and Yu, H. and Ta, T. T. H. and Tran, V. N. and Wan, S.
    Physical Chemistry Chemical Physics 20 (11) :7819–7835, 2018
  59. Transition State-Based ST6Gal I Inhibitors: Mimicking the Phosphodiester Linkage with a Triazole or Carbamate through an Enthalpy-Entropy Compensation
    Montgomery, Andrew P. and Skropeta, Danielle and Yu, Haibo
    Scientific Reports 7 (1) :14428, 2017
  60. Theoretical pK Prediction of the α-Phosphate Moiety of Uridine 5\prime-Diphosphate-GlcNAc
    Vipperla, Bhavaniprasad and Griffiths, Thomas M. and Wang, Xingyong and Yu, Haibo
    Chemical Physics Letters 667 :221–225, 2017
  61. Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design
    Montgomery, Andrew P. and Xiao, Kela and Wang, Xingyong and Skropeta, Danielle and Yu, Haibo
    In Advances in Protein Chemistry and Structural Biology, Editors: , 109 pages 25–76 , Elsevier , 2017
  62. Ammonium Aminodiboranate: A Long-Sought Isomer of Diammoniate of Diborane and Ammonia Borane Dimer
    Chen, Weidong and Yu, Haibo and Wu, Guotao and He, Teng and Li, Zhao and Guo, Zaiping and Liu, Huakun and Huang, Zhenguo and Chen, Ping
    Chemistry – a European Journal 22 (23) :7727–7729, 2016
  63. Computational Characterisation of the Interactions between Human ST6Gal I and Transition-State Analogue Inhibitors: Insights for Inhibitor Design: Molecular Modelling of Human ST6Gal I-inhibitor Complexes
    Montgomery, Andrew and Szabo, Rémi and Skropeta, Danielle and Yu, Haibo
    Journal of Molecular Recognition 29 (5) :211–222, 2016
  64. Selective Binding Modes and Allosteric Inhibitory Effects of Lupane Triterpenes on Protein Tyrosine Phosphatase 1B
    Jin, Tiantian and Yu, Haibo and Huang, Xu-Feng
    Scientific Reports 6 (1) :20766, 2016
  65. Rationalising pK\textsubscripta Shifts in Bacillus Circulans Xylanase with Computational Studies
    Xiao, Kela and Yu, Haibo
    Physical Chemistry Chemical Physics 18 (44) :30305–30312, 2016
  66. Identification of Chikungunya Virus nsP2 Protease Inhibitors Using Structure-Base Approaches
    Nguyen, Phuong T.V. and Yu, Haibo and Keller, Paul A.
    Journal of Molecular Graphics and Modelling 57 :1–8, 2015
  67. In Silico Enzyme Modelling
    Zhu, X and Yang, Y and Yu, H
    Australian Biochemist 45 (2) :12–15, 2014
  68. pKa Cycling of the General Acid/Base in Glycoside Hydrolase Families 33 and 34
    Yu, Haibo and Griffiths, Thomas M.
    Physical Chemistry Chemical Physics 16 (12) :5785, 2014
  69. Simulation Study of Ion Pairing in Concentrated Aqueous Salt Solutions with a Polarizable Force Field
    Luo, Yun and Jiang, Wei and Yu, Haibo and MacKerell, Alexander D. and Roux, Benoît
    Faraday Discuss. 160 :135–149, 2013
  70. Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations
    Daily, Michael D. and Yu, Haibo and Phillips, George N. and Cui, Qiang
    In , Editors: Klinman, Judith and Hammes- Schiffer, Sharon , Berlin, Heidelberg , 337 pages 139–164 , Springer Berlin Heidelberg , 2013
  71. Protonation of Key Acidic Residues Is Critical for the K+-Selectivity of the Na/K Pump
    Yu, Haibo and Ratheal, Ian M and Artigas, Pablo and Roux, Benoît
    Nature Structural & Molecular Biology 18 (10) :1159–1163, 2011
  72. Ion Selectivity in Channels and Transporters
    Roux, Benoît and Bernèche, Simon and Egwolf, Bernhard and Lev, Bogdan and Noskov, Sergei Y. and Rowley, Christopher N. and Yu, Haibo
    Journal of General Physiology 137 (5) :415–426, 2011
  73. Two Mechanisms of Ion Selectivity in Protein Binding Sites
    Yu, Haibo and Noskov, Sergei Yu. and Roux, Benoît
    Proceedings of the National Academy of Sciences 107 (47) :20329–20334, 2010
  74. Selectivity of Externally Facing Ion-Binding Sites in the Na/K Pump to Alkali Metals and Organic Cations
    Ratheal, Ian M. and Virgin, Gail K. and Yu, Haibo and Roux, Benoît and Gatto, Craig and Artigas, Pablo
    Proceedings of the National Academy of Sciences 107 (43) :18718–18723, 2010
  75. A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N -Methylacetamide
    Yu, Haibo and Mazzanti, Christopher L. and Whitfield, Troy W. and Koeppe, Roger E. and Andersen, Olaf S. and Roux, Benoît
    Journal of the American Chemical Society 132 (31) :10847–10856, 2010
  76. Assessing the Accuracy of Approximate Treatments of Ion Hydration Based on Primitive Quasichemical Theory
    Roux, Benoît and Yu, Haibo
    The Journal of Chemical Physics 132 (23) :234101, 2010
  77. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field
    Yu, Haibo and Whitfield, Troy W. and Harder, Edward and Lamoureux, Guillaume and Vorobyov, Igor and Anisimov, Victor M. and MacKerell, Alexander D. and Roux, Benoît
    Journal of Chemical Theory and Computation 6 (3) :774–786, 2010

Peer-reviewed Articles (before 2010)

  1. On the Utilization of Energy Minimization to the Study of Ion Selectivity
    Yu, Haibo and Roux, Benoît
    Biophysical Journal 97 (8) :L15-L17, 2009
  2. Mechanochemical Coupling in Molecular Motors: Insights from Molecular Simulations of the Myosin Motor Domain
    Yu, Haibo and Yang, Yang and Ma, Liang and Cui, Qiang
    In , Editors: Leitner, David M and Straub, John E pages 23–46 , CRC Press , 2009
  3. Hydration Number, Topological Control, and Ion Selectivity
    Yu, Haibo and Noskov, Sergei Yu. and Roux, Benoît
    The Journal of Physical Chemistry B 113 (25) :8725–8730, 2009
  4. Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization
    Yang, Yang and Yu, Haibo and York, Darrin and Elstner, Marcus and Cui, Qiang
    Journal of Chemical Theory and Computation 4 (12) :2067–2084, 2008
  5. Amino Acids with an Intermolecular Proton Bond as Proton Storage Site in Bacteriorhodopsin
    Phatak, Prasad and Ghosh, Nilanjan and Yu, Haibo and Cui, Qiang and Elstner, Marcus
    Proceedings of the National Academy of Sciences 105 (50) :19672–19677, 2008
  6. Extensive Conformational Transitions Are Required to Turn on ATP Hydrolysis in Myosin
    Yang, Yang and Yu, Haibo and Cui, Qiang
    Journal of Molecular Biology 381 (5) :1407–1420, 2008
  7. Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation
    Li, Zhenyu and Yu, Haibo and Zhuang, Wei and Mukamel, Shaul
    Chemical Physics Letters 452 (1-3) :78–83, 2008
  8. Molecular Dynamics Simulation of Human Interleukin-4: Comparison with NMR Data and Effect of pH, Counterions and Force Field on Tertiary Structure Stability
    Winger, M. and Yu, H. and Redfield, C. and Van Gunsteren, W. F.
    Molecular Simulation 33 (14) :1143–1154, 2007
  9. The Vibrational Spectra of Protonated Water Clusters: A Benchmark for Self-Consistent-Charge Density-Functional Tight Binding
    Yu, Haibo and Cui, Qiang
    The Journal of Chemical Physics 127 (23) :234504, 2007
  10. 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
    Yang, Yang and Yu, Haibo and York, Darrin and Cui, Qiang and Elstner, Marcus
    The Journal of Physical Chemistry a 111 (42) :10861–10873, 2007
  11. Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations
    Yu, Haibo and Ma, Liang and Yang, Yang and Cui, Qiang
    PLOS Computational Biology 3 (2) :e21, 2007
  12. Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues
    Yu, Haibo and Ma, Liang and Yang, Yang and Cui, Qiang
    PLOS Computational Biology 3 (2) :e23, 2007
  13. “Proton Holes” in Long-Range Proton Transfer Reactions in Solution and Enzymes: A Theoretical Analysis
    Riccardi, Demian and König, Peter and Prat-Resina, Xavier and Yu, Haibo and Elstner, Marcus and Frauenheim, Thomas and Cui, Qiang
    Journal of the American Chemical Society 128 (50) :16302–16311, 2006
  14. Molecular Dynamics Study of the Stabilities of Consensus Designed Ankyrin Repeat Proteins
    Yu, Haibo and Kohl, Andreas and Binz, H. Kaspar and Plückthun, Andreas and Grütter, Markus G. and Van Gunsteren, Wilfred F.
    Proteins: Structure, Function, and Bioinformatics 65 (2) :285–295, 2006
  15. Molecular Dynamics Simulations of Liquid Methanol and Methanol–Water Mixtures with Polarizable Models
    Yu, Haibo and Geerke, Daan P. and Liu, Haiyan and Van Gunsteren, Wilfred F.
    Journal of Computational Chemistry 27 (13) :1494–1504, 2006
  16. Biomolecular Modeling: Goals, Problems, Perspectives
    Van Gunsteren, Wilfred F. and Bakowies, Dirk and Baron, Riccardo and Chandrasekhar, Indira and Christen, Markus and Daura, Xavier and Gee, Peter and Geerke, Daan P. and Glättli, Alice and Hünenberger, Philippe H. and Kastenholz, Mika A. and Oostenbrink, Chris and Schenk, Merijn and Trzesniak, Daniel and Van Der Vegt, Nico F. A. and Yu, Haibo B.
    Angewandte Chemie International Edition 45 (25) :4064–4092, 2006
  17. Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes
    Riccardi, Demian and Schaefer, Patricia and Yang and Yu, Haibo and Ghosh, Nilanjan and Prat-Resina, Xavier and König, Peter and Li, Guohui and Xu, Dingguo and Guo, Hua and Elstner, Marcus and Cui, Qiang
    The Journal of Physical Chemistry B 110 (13) :6458–6469, 2006
  18. Accounting for Polarization in Molecular Simulation
    Yu, Haibo and Van Gunsteren, Wilfred F.
    Computer Physics Communications 172 (2) :69–85, 2005
  19. Charge-on-Spring Polarizable Water Models Revisited: From Water Clusters to Liquid Water to Ice
    Yu, Haibo and Van Gunsteren, Wilfred F.
    The Journal of Chemical Physics 121 (19) :9549–9564, 2004
  20. Effect of Methylation on the Stability and Solvation Free Energy of Amylose and Cellulose Fragments: A Molecular Dynamics Study
    Yu, Haibo and Amann, Manfred and Hansson, Tomas and Köhler, Jutta and Wich, Günter and Van Gunsteren, Wilfred F.
    Carbohydrate Research 339 (10) :1697–1709, 2004
  21. Comparison of Properties of Aib-Rich Peptides in Crystal and Solution: A Molecular Dynamics Study
    Yu, Haibo and Ramseier, Maaike and Bürgi, Roland and Van Gunsteren, Wilfred F.
    ChemPhysChem 5 (5) :633–641, 2004
  22. On the Transferability of the SPC/L Water Model to Biomolecular Simulation
    Glättli, Alice and Oostenbrink, Chris and Daura, Xavier and Geerke, Daan P. and Yu, Haibo and Van Gunsteren, Wilfred F.
    Brazilian Journal of Physics 34 (1) :116–125, 2004
  23. Molecular Dynamics Simulations of Peptides Containing an Unnatural Amino Acid: Dimerization, Folding, and Protein Binding
    Yu, Haibo and Daura, Xavier and Van Gunsteren, Wilfred F.
    Proteins: Structure, Function, and Bioinformatics 54 (1) :116–127, 2004
  24. Development of a Simple, Self-Consistent Polarizable Model for Liquid Water
    Yu, Haibo and Hansson, Tomas and Van Gunsteren, Wilfred F.
    The Journal of Chemical Physics 118 (1) :221–234, 2003
  25. Molecular Dynamics Simulation of Biomolecular Systems
    Van Gunsteren, Wilfred and Bakowies, Dirk and Bürgi, Roland and Chandrasekhar, Indira and Christen, Markus and Daura, Xavier and Gee, Peter and Glättli, Alice and Hansson, Tomas and Oostenbrink, Chris and Pitera, Jed and Peter, Christine and Schuler, Lukas and Soares, Thereza and Yu, Haibo
    Chimia 55 (10) :856–860, 2001
  26. Design of New Selective Inhibitors of Cyclooxygenase-2 by Dynamic Assembly of Molecular Building Blocks
    Zhu, Jiang and Yu, Haibo and Fan, Hao and Liu, Haiyan and Shi, Yunyu
    Journal of Computer-Aided Molecular Design 15 (5) :447–463, 2001