Haibo Yu - Publications

University of Wollongong, Australia 
computational chemistry and biophysics

54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Gao P, Huang Z, Yu H. Exploration of the Dehydrogenation Pathways of Ammonia Diborane and Diammoniate of Diborane by Molecular Dynamics Simulations Using Reactive Force Fields. The Journal of Physical Chemistry. A. PMID 32045237 DOI: 10.1021/Acs.Jpca.9B10441  0.308
2020 Inakollu VS, Geerke DP, Rowley CN, Yu H. Polarisable force fields: what do they add in biomolecular simulations? Current Opinion in Structural Biology. 61: 182-190. PMID 32044671 DOI: 10.1016/J.Sbi.2019.12.012  0.622
2019 Luna-Ramirez K, Csoti A, McArthur JR, Chin YKY, Anangi R, Del Carmen Najera R, Possani LD, King GF, Panyi G, Yu H, Adams DJ, Finol-Urdaneta RK. Structural basis of the potency and selectivity of Urotoxin, a potent Kv1 blocker from scorpion venom. Biochemical Pharmacology. 113782. PMID 31881193 DOI: 10.1016/J.Bcp.2019.113782  0.304
2019 Griffiths TM, Oakley AJ, Yu H. Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. Journal of Computational Chemistry. PMID 31840840 DOI: 10.1002/Jcc.26125  0.74
2019 Awoonor-Williams E, Isley WC, Dale SG, Johnson ER, Yu H, Becke AD, Roux B, Rowley CN. Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. Journal of Computational Chemistry. PMID 31512279 DOI: 10.1002/Jcc.26064  0.691
2019 Chen Y, Wang X, Lao M, Rui K, Zheng X, Yu H, Ma J, Dou SX, Sun W. Electrocatalytically inactive SnS2 promotes water adsorption/dissociation on molybdenum dichalcogenides for accelerated alkaline hydrogen evolution Nano Energy. 64: 103918. DOI: 10.1016/J.Nanoen.2019.103918  0.308
2018 Zhao G, Wang X, Wang S, Rui K, Chen Y, Yu H, Ma J, Dou SX, Sun W. Heteroatom-doped MoSe2 nanosheets with enhanced hydrogen evolution kinetics for alkaline water splitting. Chemistry, An Asian Journal. PMID 30508277 DOI: 10.1002/Asia.201801645  0.318
2018 Poad BLJ, Maccarone AT, Yu H, Mitchell TW, M Saied E, Arenz C, Hornemann T, Bull JN, Bieske EJ, Blanksby SJ. Differential-mobility spectrometry of 1-deoxysphingosine isomers: new insights into the gas phase structures of ionized lipids. Analytical Chemistry. PMID 29608293 DOI: 10.1021/Acs.Analchem.8B00469  0.313
2017 Montgomery AP, Skropeta D, Yu H. Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation. Scientific Reports. 7: 14428. PMID 29089525 DOI: 10.1038/S41598-017-14560-0  0.339
2017 Vipperla B, Griffiths TM, Wang X, Yu H. Theoretical pK prediction of the α-phosphate moiety of uridine 5′-diphosphate-GlcNAc Chemical Physics Letters. 667: 220-225. DOI: 10.1016/J.Cplett.2016.12.001  0.727
2016 Xiao K, Yu H. Rationalising pKa shifts in Bacillus circulans xylanase with computational studies. Physical Chemistry Chemical Physics : Pccp. PMID 27485091 DOI: 10.1039/C6Cp02526A  0.372
2016 Jin T, Yu H, Huang XF. Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B. Scientific Reports. 6: 20766. PMID 26865097 DOI: 10.1038/Srep20766  0.322
2015 Montgomery A, Szabo R, Skropeta D, Yu H. Computational characterisation of the interactions between human ST6Gal I and transition-state analogue inhibitors: insights for inhibitor design. Journal of Molecular Recognition : Jmr. PMID 26669681 DOI: 10.1002/Jmr.2520  0.331
2015 Nguyen PT, Yu H, Keller PA. Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches. Journal of Molecular Graphics & Modelling. 57: 1-8. PMID 25622129 DOI: 10.1016/J.Jmgm.2015.01.001  0.339
2014 Yu H, Griffiths TM. pKa cycling of the general acid/base in glycoside hydrolase families 33 and 34. Physical Chemistry Chemical Physics : Pccp. 16: 5785-92. PMID 24535426 DOI: 10.1039/C4Cp00351A  0.73
2013 Luo Y, Jiang W, Yu H, MacKerell AD, Roux B. Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field. Faraday Discussions. 160: 135-49; discussion 2. PMID 23795497 DOI: 10.1039/C2Fd20068F  0.595
2013 Daily MD, Yu H, Phillips GN, Cui Q. Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations. Topics in Current Chemistry. 337: 139-64. PMID 23468286 DOI: 10.1007/128_2012_409  0.47
2013 Yang L, Chao C, Tang W, Wang Z, Yu H, Cui Q, Zhou Z. [Effect of cryopreservation method on islets specific T cell responses in type 1 diabetic patient]. Zhong Nan Da Xue Xue Bao. Yi Xue Ban = Journal of Central South University. Medical Sciences. 38: 169-75. PMID 23456066 DOI: 10.3969/j.issn.1672-7347.2013.02.010  0.325
2012 Yu H, Ratheal I, Artigas P, Roux B. Molecular mechanisms of K + selectivity in Na/K pump Australian Journal of Chemistry. 65: 448-456. DOI: 10.1071/Ch12026  0.492
2011 Yu H, Ratheal IM, Artigas P, Roux B. Protonation of key acidic residues is critical for the K⁺-selectivity of the Na/K pump. Nature Structural & Molecular Biology. 18: 1159-63. PMID 21909093 DOI: 10.1038/Nsmb.2113  0.491
2011 Roux B, Bernèche S, Egwolf B, Lev B, Noskov SY, Rowley CN, Yu H. Ion selectivity in channels and transporters. The Journal of General Physiology. 137: 415-26. PMID 21518830 DOI: 10.1085/Jgp.201010577  0.713
2011 Cordero-Morales JF, Jogini V, Vasquez V, Bourdeau RW, Yu H, Roux B, Tristani-Firouzi M, Perozo E. Engineering the hERG1 Selectivity Filter into the NaK Pore Domain Biophysical Journal. 100: 584a. DOI: 10.1016/J.Bpj.2010.12.3372  0.458
2010 Yu H, Noskov SY, Roux B. Two mechanisms of ion selectivity in protein binding sites. Proceedings of the National Academy of Sciences of the United States of America. 107: 20329-34. PMID 21057111 DOI: 10.1073/Pnas.1007150107  0.648
2010 Ratheal IM, Virgin GK, Yu H, Roux B, Gatto C, Artigas P. Selectivity of externally facing ion-binding sites in the Na/K pump to alkali metals and organic cations. Proceedings of the National Academy of Sciences of the United States of America. 107: 18718-23. PMID 20937860 DOI: 10.1073/Pnas.1004214107  0.505
2010 Yu H, Mazzanti CL, Whitfield TW, Koeppe RE, Andersen OS, Roux B. A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide. Journal of the American Chemical Society. 132: 10847-56. PMID 20681718 DOI: 10.1021/Ja103270W  0.547
2010 Roux B, Yu H. Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory. The Journal of Chemical Physics. 132: 234101. PMID 20572683 DOI: 10.1063/1.3436632  0.537
2010 Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, Mackerell AD, Roux B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. Journal of Chemical Theory and Computation. 6: 774-786. PMID 20300554 DOI: 10.1021/Ct900576A  0.655
2010 Virgin G, Ratheal I, Yaragatupalli S, Yu H, Roux B, Gatto C, Artigas P. Ion-Selectivity of Externally Facing Na+-Exclusive and Na+/K+-Shared Sites in the Na/K-Pump Biophysical Journal. 98: 168a. DOI: 10.1016/J.Bpj.2009.12.909  0.466
2010 Yu H, Noskov SY, Roux B. The Role of Architectural and Structural Forces in Ion Selectivity Biophysical Journal. 98: 330a. DOI: 10.1016/J.Bpj.2009.12.1790  0.651
2010 Yu H, Artigas P, Roux B. Microscopic Mechanism of Ion Selectivity in the Nak Pump Biophysical Journal. 98: 330a. DOI: 10.1016/J.Bpj.2009.12.1789  0.518
2009 Yu H, Roux B. On the utilization of energy minimization to the study of ion selectivity. Biophysical Journal. 97: L15-7. PMID 19843443 DOI: 10.1016/J.Bpj.2009.08.005  0.512
2009 Yu H, Noskov SY, Roux B. Hydration number, topological control, and ion selectivity. The Journal of Physical Chemistry. B. 113: 8725-30. PMID 19489546 DOI: 10.1021/Jp901233V  0.65
2009 Yu H, Whitfield TW, Noskov SY, Mazzanti CL, Koeppe RE, Andersen OS, Roux B. Development of a Drude Polarizable Force Field for Ion-water and Ion-NMA Interactions and Application to Selectivity in Ion Channels Biophysical Journal. 96: 660a. DOI: 10.1016/J.Bpj.2008.12.3488  0.66
2008 Yang Y, Yu H, York D, Elstner M, Cui Q. Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization. Journal of Chemical Theory and Computation. 4: 2067-2084. PMID 19352441 DOI: 10.1021/Ct800330D  0.515
2008 Phatak P, Ghosh N, Yu H, Cui Q, Elstner M. Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 105: 19672-7. PMID 19064907 DOI: 10.1073/Pnas.0810712105  0.638
2008 Yang Y, Yu H, Cui Q. Extensive conformational transitions are required to turn on ATP hydrolysis in myosin. Journal of Molecular Biology. 381: 1407-20. PMID 18619975 DOI: 10.1016/J.Jmb.2008.06.071  0.499
2008 Li Z, Yu H, Zhuang W, Mukamel S. Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation. Chemical Physics Letters. 452: 78-83. PMID 18438457 DOI: 10.1016/J.Cplett.2007.12.022  0.319
2007 Yu H, Cui Q. The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding. The Journal of Chemical Physics. 127: 234504. PMID 18154397 DOI: 10.1063/1.2806992  0.506
2007 Yang Y, Yu H, York D, Cui Q, Elstner M. 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. The Journal of Physical Chemistry. A. 111: 10861-73. PMID 17914769 DOI: 10.1021/Jp074167R  0.471
2007 Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues. Plos Computational Biology. 3: e23. PMID 17305418 DOI: 10.1371/Journal.Pcbi.0030023  0.558
2007 Yu H, Ma L, Yang Y, Cui Q. Mechanochemical coupling in the myosin motor domain. I. Insights from equilibrium active-site simulations. Plos Computational Biology. 3: e21. PMID 17291159 DOI: 10.1371/Journal.Pcbi.0030021  0.554
2007 Winger M, Yu H, Redfield C, Van Gunsteren WF. Molecular dynamics simulation of human interleukin-4: Comparison with NMR data and effect of pH, counterions and force field on tertiary structure stability Molecular Simulation. 33: 1143-1154. DOI: 10.1080/08927020701613623  0.49
2006 Riccardi D, König P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, Cui Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. Journal of the American Chemical Society. 128: 16302-11. PMID 17165785 DOI: 10.1021/Ja065451J  0.653
2006 Yu H, Kohl A, Binz HK, Plückthun A, Grütter MG, van Gunsteren WF. Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins. Proteins. 65: 285-95. PMID 16948156 DOI: 10.1002/Prot.20991  0.469
2006 Yu H, Geerke DP, Liu H, van Gunsteren WF. Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. Journal of Computational Chemistry. 27: 1494-504. PMID 16838298 DOI: 10.1002/Jcc.20429  0.51
2006 van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NF, ... Yu HB, et al. Biomolecular modeling: Goals, problems, perspectives. Angewandte Chemie (International Ed. in English). 45: 4064-92. PMID 16761306 DOI: 10.1002/Anie.200502655  0.581
2006 Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, König P, Li G, Xu D, Guo H, Elstner M, Cui Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. The Journal of Physical Chemistry. B. 110: 6458-69. PMID 16570942 DOI: 10.1021/Jp056361O  0.726
2005 Yu H, van Gunsteren WF. Accounting for polarization in molecular simulation Computer Physics Communications. 172: 69-85. DOI: 10.1016/J.Cpc.2005.01.022  0.517
2004 Yu H, van Gunsteren WF. Charge-on-spring polarizable water models revisited: from water clusters to liquid water to ice. The Journal of Chemical Physics. 121: 9549-64. PMID 15538877 DOI: 10.1063/1.1805516  0.496
2004 Yu H, Amann M, Hansson T, Köhler J, Wich G, van Gunsteren WF. Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study. Carbohydrate Research. 339: 1697-709. PMID 15220079 DOI: 10.1016/J.Carres.2004.05.003  0.484
2004 Yu H, Ramseier M, Bürgi R, van Gunsteren WF. Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 5: 633-41. PMID 15179715 DOI: 10.1002/Cphc.200301026  0.486
2004 Yu H, Daura X, van Gunsteren WF. Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding. Proteins. 54: 116-27. PMID 14705028 DOI: 10.1002/Prot.10502  0.483
2004 Glättli A, Oostenbrink C, Daura X, Geerke DP, Yu H, van Gunsteren WF. On the transferability of the SPC/L water model to biomolecular simulation Brazilian Journal of Physics. 34: 116-125. DOI: 10.1590/S0103-97332004000100015  0.558
2001 Zhu J, Yu H, Fan H, Liu H, Shi Y. Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks Journal of Computer-Aided Molecular Design. 15: 447-463. PMID 11394738 DOI: 10.1023/A:1011114307711  0.566
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