| Year |
Citation |
Score |
| 2024 |
El Salamouni NS, Buckley BJ, Lee R, Ranson M, Kelso MJ, Yu H. Ion Transport and Inhibitor Binding by Human NHE1: Insights from Molecular Dynamics Simulations and Free Energy Calculations. The Journal of Physical Chemistry. B. 128: 440-450. PMID 38185879 DOI: 10.1021/acs.jpcb.3c05863 |
0.309 |
|
| 2022 |
Newing TP, Brewster JL, Fitschen LJ, Bouwer JC, Johnston NP, Yu H, Tolun G. Redβ annealase structure reveals details of oligomerization and λ Red-mediated homologous DNA recombination. Nature Communications. 13: 5649. PMID 36163171 DOI: 10.1038/s41467-022-33090-6 |
0.734 |
|
| 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 |
0.311 |
|
| 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 |
0.616 |
|
| 2020 |
Ta HT, Tieu AK, Zhu H, Yu H, Tran NV, Tran BH, Wan S, Ta TD. Ab initio study on physical and chemical interactions at borates and iron oxide interface at high temperature Chemical Physics. 529: 110548. DOI: 10.1016/J.Chemphys.2019.110548 |
0.322 |
|
| 2020 |
Fan H, Wang X, Yu H, Gu Q, Chen S, Liu Z, Chen X, Luo W, Liu H. Enhanced Potassium Ion Battery by Inducing Interlayer Anionic Ligands in MoS1.5Se0.5 Nanosheets with Exploration of the Mechanism Advanced Energy Materials. 10: 1904162. DOI: 10.1002/Aenm.201904162 |
0.316 |
|
| 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 |
0.305 |
|
| 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 |
0.689 |
|
| 2019 |
Xiao K, Wang X, Yu H. Comparative studies of catalytic pathways for Streptococcus pneumoniae sialidases NanA, NanB and NanC. Scientific Reports. 9: 2157. PMID 30770840 DOI: 10.1038/S41598-018-38131-Z |
0.328 |
|
| 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 |
0.305 |
|
| 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 |
0.314 |
|
| 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 |
0.314 |
|
| 2018 |
Wang X, Yu L, Inakollu VSS, Pan X, Ma J, Yu H. Molecular Quantum Dot Cellular Automata Based on Diboryl Monoradical Anions Journal of Physical Chemistry C. 122: 1. DOI: 10.1021/Acs.Jpcc.7B11964 |
0.309 |
|
| 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 |
0.34 |
|
| 2017 |
Montgomery AP, Xiao K, Wang X, Skropeta D, Yu H. Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design. Advances in Protein Chemistry and Structural Biology. 109: 25-76. PMID 28683920 DOI: 10.1016/Bs.Apcsb.2017.04.003 |
0.302 |
|
| 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 |
0.725 |
|
| 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 |
0.321 |
|
| 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 |
0.333 |
|
| 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 |
0.345 |
|
| 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 |
0.728 |
|
| 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 |
0.586 |
|
| 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 |
0.465 |
|
| 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 |
0.315 |
|
| 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 |
0.484 |
|
| 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 |
0.483 |
|
| 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 |
0.708 |
|
| 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 |
0.454 |
|
| 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 |
0.642 |
|
| 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 |
0.497 |
|
| 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 |
0.542 |
|
| 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 |
0.528 |
|
| 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 |
0.65 |
|
| 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 |
0.457 |
|
| 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 |
0.644 |
|
| 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 |
0.51 |
|
| 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 |
0.503 |
|
| 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 |
0.644 |
|
| 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 |
0.654 |
|
| 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 |
0.511 |
|
| 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 |
0.634 |
|
| 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 |
0.498 |
|
| 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 |
0.312 |
|
| 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 |
0.5 |
|
| 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 |
0.468 |
|
| 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 |
0.55 |
|
| 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 |
0.546 |
|
| 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 |
0.487 |
|
| 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 |
0.648 |
|
| 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 |
0.472 |
|
| 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 |
0.508 |
|
| 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 |
0.575 |
|
| 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 |
0.723 |
|
| 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 |
0.514 |
|
| 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 |
0.492 |
|
| 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 |
0.487 |
|
| 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 |
0.486 |
|
| 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 |
0.55 |
|
| 2003 |
Yu H, Hansson T, Van Gunsteren WF. Development of a simple, self-consistent polarizable model for liquid water Journal of Chemical Physics. 118: 221-234. DOI: 10.1063/1.1523915 |
0.314 |
|
| 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 |
0.56 |
|
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