| Year |
Citation |
Score |
| 2020 |
Wang J, Peng C, Yu Y, Chen Z, Xu Z, Cai T, Shao Q, Shi J, Zhu W. Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation. Biophysical Journal. PMID 31995738 DOI: 10.1016/J.Bpj.2020.01.001 |
0.433 |
|
| 2019 |
Shao Q, Zhu W. Exploring Ligand Binding/Unbinding Pathway by Enhanced Sampling Selectively of Ligand in Protein-Ligand Complex. The Journal of Physical Chemistry. B. PMID 31478672 DOI: 10.1021/Acs.Jpcb.9B05226 |
0.357 |
|
| 2019 |
Yang YI, Shao Q, Zhang J, Yang L, Gao YQ. Enhanced sampling in molecular dynamics. The Journal of Chemical Physics. 151: 070902. PMID 31438687 DOI: 10.1063/1.5109531 |
0.624 |
|
| 2019 |
Shao Q, Zhu W. Nonnative contact effects in protein folding. Physical Chemistry Chemical Physics : Pccp. PMID 31134232 DOI: 10.1039/C8Cp07524G |
0.445 |
|
| 2019 |
Shao Q, Yang L, Zhu W. Selective enhanced sampling in dihedral energy facilitates overcoming the dihedral energy increase in protein folding and accelerates the searching for protein native structure. Physical Chemistry Chemical Physics : Pccp. PMID 31066393 DOI: 10.1039/C9Cp00615J |
0.436 |
|
| 2019 |
Shao Q, Zhu W. Ligand binding effects on the activation of the EGFR extracellular domain. Physical Chemistry Chemical Physics : Pccp. PMID 30933195 DOI: 10.1039/C8Cp07496H |
0.304 |
|
| 2019 |
Liu Y, Sun C, Han L, Yu Y, Zhou H, Shao Q, Lou J, Zhao Y, Huang Y. Conformational dynamics, intramolecular domain conformation signaling and activation of apo-FimD revealed by single-molecule FRET studies. Biochemistry. PMID 30888187 DOI: 10.1021/Acs.Biochem.9B00080 |
0.37 |
|
| 2018 |
Shao Q, Zhu W. The effects of implicit modeling of nonpolar solvation on protein folding simulations. Physical Chemistry Chemical Physics : Pccp. PMID 29946610 DOI: 10.1039/C8Cp03156H |
0.443 |
|
| 2018 |
Shao Q, Zhu W. Assessing AMBER force fields for protein folding in an implicit solvent. Physical Chemistry Chemical Physics : Pccp. PMID 29480910 DOI: 10.1039/C7Cp08010G |
0.425 |
|
| 2017 |
Shao Q, Zhu W. How Well Can Implicit Solvent Simulations Explore Folding Pathway? A Quantitative Analysis of α-Helix Bundle Proteins. Journal of Chemical Theory and Computation. PMID 29120630 DOI: 10.1021/Acs.Jctc.7B00726 |
0.444 |
|
| 2017 |
Shao Q, Zhu W. Effective Conformational Sampling in Explicit Solvent with Gaussian Biased Accelerated Molecular Dynamics. Journal of Chemical Theory and Computation. PMID 28759210 DOI: 10.1021/Acs.Jctc.7B00242 |
0.478 |
|
| 2017 |
Shao Q, Shi J, Zhu W. Determining Protein Folding Pathway and Associated Energetics through Partitioned Integrated-Tempering-Sampling Simulation. Journal of Chemical Theory and Computation. PMID 28121433 DOI: 10.1021/Acs.Jctc.6B00967 |
0.441 |
|
| 2016 |
Shao Q, Xu Z, Wang J, Shi J, Zhu W. Energetics and structural characterization of the "DFG-flip" conformational transition of B-RAF kinase: a SITS molecular dynamics study. Physical Chemistry Chemical Physics : Pccp. PMID 27966693 DOI: 10.1039/C6Cp06624K |
0.382 |
|
| 2016 |
Shao Q. Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions. Physical Chemistry Chemical Physics : Pccp. PMID 27730231 DOI: 10.1039/C6Cp05634B |
0.436 |
|
| 2016 |
Chen Z, Wang G, Xu Z, Wang J, Yu Y, Cai T, Shao Q, Shi J, Zhu W. How do Distance and Solvent Affect the Halogen Bonding Involving Negatively Charged Donors? The Journal of Physical Chemistry. B. PMID 27504672 DOI: 10.1021/Acs.Jpcb.6B05027 |
0.337 |
|
| 2016 |
Yu Y, Wang J, Shao Q, Shi J, Zhu W. The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: a microscopic view. Scientific Reports. 6: 19500. PMID 26775871 DOI: 10.1038/Srep19500 |
0.412 |
|
| 2015 |
Yu Y, Wang J, Shao Q, Shi J, Zhu W. Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir. Scientific Reports. 5: 10517. PMID 26012849 DOI: 10.1038/Srep10517 |
0.322 |
|
| 2015 |
Yu Y, Wang J, Shao Q, Shi J, Zhu W. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation. The Journal of Chemical Physics. 142: 125105. PMID 25833612 DOI: 10.1063/1.4916118 |
0.437 |
|
| 2015 |
Yang L, Liu CW, Shao Q, Zhang J, Gao YQ. From thermodynamics to kinetics: enhanced sampling of rare events. Accounts of Chemical Research. 48: 947-55. PMID 25781363 DOI: 10.1021/Ar500267N |
0.637 |
|
| 2015 |
Wang J, Shao Q, Cossins BP, Shi J, Chen K, Zhu W. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters. Journal of Biomolecular Structure & Dynamics. 1-14. PMID 25761118 DOI: 10.1080/07391102.2015.1019928 |
0.361 |
|
| 2015 |
Shao Q. Folding or misfolding: the choice of β-hairpin. The Journal of Physical Chemistry. B. 119: 3893-900. PMID 25692381 DOI: 10.1021/Jp5100654 |
0.401 |
|
| 2015 |
Xiong X, Chen Z, Cossins BP, Xu Z, Shao Q, Ding K, Zhu W, Shi J. Force fields and scoring functions for carbohydrate simulation. Carbohydrate Research. 401: 73-81. PMID 25464084 DOI: 10.1016/J.Carres.2014.10.028 |
0.376 |
|
| 2015 |
Shao Q. Important roles of hydrophobic interactions in folding and charge interactions in misfolding of α-helix bundle protein Rsc Advances. 5: 4191-4199. DOI: 10.1039/C4Ra14265A |
0.43 |
|
| 2014 |
Wang J, Peng S, Cossins BP, Liao X, Chen K, Shao Q, Zhu X, Shi J, Zhu W. Mapping central α-helix linker mediated conformational transition pathway of calmodulin via simple computational approach. The Journal of Physical Chemistry. B. 118: 9677-85. PMID 25120210 DOI: 10.1021/Jp507186H |
0.345 |
|
| 2014 |
Shao Q. Methanol concentration dependent protein denaturing ability of guanidinium/methanol mixed solution. The Journal of Physical Chemistry. B. 118: 6175-85. PMID 24846320 DOI: 10.1021/Jp500280V |
0.436 |
|
| 2014 |
Shao Q. Probing sequence dependence of folding pathway of α-helix bundle proteins through free energy landscape analysis. The Journal of Physical Chemistry. B. 118: 5891-900. PMID 24837534 DOI: 10.1021/Jp5043393 |
0.394 |
|
| 2014 |
Wang J, Shao Q, Xu Z, Liu Y, Yang Z, Cossins BP, Jiang H, Chen K, Shi J, Zhu W. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics. The Journal of Physical Chemistry. B. 118: 134-43. PMID 24350625 DOI: 10.1021/Jp4105129 |
0.405 |
|
| 2014 |
Shao Q. The addition of 2,2,2-trifluoroethanol prevents the aggregation of guanidinium around protein and impairs its denaturation ability: a molecular dynamics simulation study. Proteins. 82: 944-53. PMID 24214542 DOI: 10.1002/Prot.24468 |
0.435 |
|
| 2014 |
Shao Q, Wang J, Zhu W. On the influence of the mixture of denaturants on protein structure stability: A molecular dynamics study Chemical Physics. 441: 38-46. DOI: 10.1016/J.Chemphys.2014.07.006 |
0.426 |
|
| 2013 |
Shao Q, Wang J, Shi J, Zhu W. The universality of β-hairpin misfolding indicated by molecular dynamics simulations. The Journal of Chemical Physics. 139: 165103. PMID 24182084 DOI: 10.1063/1.4826461 |
0.457 |
|
| 2013 |
Shao Q. On the influence of hydrated imidazolium-based ionic liquid on protein structure stability: a molecular dynamics simulation study. The Journal of Chemical Physics. 139: 115102. PMID 24070310 DOI: 10.1063/1.4821588 |
0.455 |
|
| 2013 |
Wang J, Fulford T, Shao Q, Javelle A, Yang H, Zhu W, Merrick M. Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction. Plos One. 8: e62745. PMID 23667517 DOI: 10.1371/Journal.Pone.0062745 |
0.361 |
|
| 2013 |
Zhang Z, Xu Z, Yang Z, Liu Y, Wang J, Shao Q, Li S, Lu Y, Zhu W. The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies. The Journal of Physical Chemistry. B. 117: 4827-35. PMID 23581492 DOI: 10.1021/Jp4001658 |
0.383 |
|
| 2013 |
Wu T, Yang L, Zhang R, Shao Q, Zhuang W. Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation. The Journal of Physical Chemistry. A. 117: 6256-63. PMID 23496267 DOI: 10.1021/Jp400625A |
0.356 |
|
| 2013 |
Shao Q, Shi J, Zhu W. Molecular dynamics simulation indicating cold denaturation of β-hairpins. The Journal of Chemical Physics. 138: 085102. PMID 23464178 DOI: 10.1063/1.4792299 |
0.434 |
|
| 2012 |
Shao Q, Fan Y, Yang L, Gao YQ. Counterion Effects on the Denaturing Activity of Guanidinium Cation to Protein. Journal of Chemical Theory and Computation. 8: 4364-4373. PMID 26605599 DOI: 10.1021/Ct3002267 |
0.537 |
|
| 2012 |
Shao Q, Zhu W, Gao YQ. Robustness in protein folding revealed by thermodynamics calculations. The Journal of Physical Chemistry. B. 116: 13848-56. PMID 23130913 DOI: 10.1021/Jp307684H |
0.547 |
|
| 2012 |
Shao Q, Gao YQ. Water plays an important role in osmolyte-induced hairpin structure change: a molecular dynamics simulation study. The Journal of Chemical Physics. 137: 145101. PMID 23061865 DOI: 10.1063/1.4757419 |
0.528 |
|
| 2012 |
Lyu ZX, Shao Q, Gao YQ, Zhao XS. Direct observation of the uptake of outer membrane proteins by the periplasmic chaperone Skp. Plos One. 7: e46068. PMID 23049938 DOI: 10.1371/Journal.Pone.0046068 |
0.551 |
|
| 2012 |
Shao Q, Shi J, Zhu W. Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein. The Journal of Chemical Physics. 137: 125103. PMID 23020351 DOI: 10.1063/1.4754656 |
0.443 |
|
| 2012 |
Shao Q, Fan Y, Yang L, Gao YQ. From protein denaturant to protectant: comparative molecular dynamics study of alcohol/protein interactions. The Journal of Chemical Physics. 136: 115101. PMID 22443795 DOI: 10.1063/1.3692801 |
0.537 |
|
| 2012 |
Shao Q, Qin Gao Y. The Protein Folding Mechanism Revealed by the Folding Free Energy Landscape Analysis and Denaturation Simulations Current Physical Chemistry. 2: 33-44. DOI: 10.2174/1877946811202010033 |
0.304 |
|
| 2012 |
Yang L, Shao Q, Gao Y. Enhanced sampling method in molecular simulations Progress in Chemistry. 24: 1199-1213. |
0.463 |
|
| 2011 |
Shao Q, Yang L, Gao YQ. Structure change of β-hairpin induced by turn optimization: an enhanced sampling molecular dynamics simulation study. The Journal of Chemical Physics. 135: 235104. PMID 22191904 DOI: 10.1063/1.3668288 |
0.563 |
|
| 2011 |
Shao Q, Gao YQ. The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation. The Journal of Chemical Physics. 135: 135102. PMID 21992340 DOI: 10.1063/1.3630127 |
0.602 |
|
| 2011 |
Hwang S, Shao Q, Williams H, Hilty C, Gao YQ. Methanol strengthens hydrogen bonds and weakens hydrophobic interactions in proteins--a combined molecular dynamics and NMR study. The Journal of Physical Chemistry. B. 115: 6653-60. PMID 21534580 DOI: 10.1021/Jp111448A |
0.575 |
|
| 2011 |
Chen L, Shao Q, Gao YQ, Russell DH. Molecular dynamics and ion mobility spectrometry study of model β-hairpin peptide, trpzip1. The Journal of Physical Chemistry. A. 115: 4427-35. PMID 21476523 DOI: 10.1021/Jp110014J |
0.501 |
|
| 2010 |
Shao Q, Wei H, Gao YQ. Effects of turn stability and side-chain hydrophobicity on the folding of β-structures. Journal of Molecular Biology. 402: 595-609. PMID 20804769 DOI: 10.1016/J.Jmb.2010.08.037 |
0.564 |
|
| 2010 |
Wei H, Shao Q, Gao YQ. The effects of side chain hydrophobicity on the denaturation of simple beta-hairpins. Physical Chemistry Chemical Physics : Pccp. 12: 9292-9. PMID 20571679 DOI: 10.1039/B924593F |
0.53 |
|
| 2010 |
Lund L, Fan Y, Shao Q, Gao YQ, Raushel FM. Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation. Journal of the American Chemical Society. 132: 3870-8. PMID 20187643 DOI: 10.1021/Ja910441V |
0.517 |
|
| 2010 |
Shao Q, Gao YQ. Temperature dependence of hydrogen-bond stability in β-hairpin structures Journal of Chemical Theory and Computation. 6: 3750-3760. DOI: 10.1021/Ct100436R |
0.502 |
|
| 2009 |
Fan Y, Lund L, Shao Q, Gao YQ, Raushel FM. A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase. Journal of the American Chemical Society. 131: 10211-9. PMID 19569682 DOI: 10.1021/Ja902557R |
0.53 |
|
| 2009 |
Shao Q, Yang L, Gao YQ. A test of implicit solvent models on the folding simulation of the GB1 peptide. The Journal of Chemical Physics. 130: 195104. PMID 19466868 DOI: 10.1063/1.3132850 |
0.54 |
|
| 2009 |
Yang L, Shao Q, Gao YQ. Comparison between integrated and parallel tempering methods in enhanced sampling simulations. The Journal of Chemical Physics. 130: 124111. PMID 19334812 DOI: 10.1063/1.3097129 |
0.517 |
|
| 2009 |
Yang L, Shao Q, Gao YQ. Thermodynamics and folding pathways of trpzip2: an accelerated molecular dynamics simulation study. The Journal of Physical Chemistry. B. 113: 803-8. PMID 19113829 DOI: 10.1021/Jp803160F |
0.601 |
|
| 2008 |
Gao YQ, Yang L, Fan Y, Shao Q. Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems International Reviews in Physical Chemistry. 27: 201-227. DOI: 10.1080/01442350801920334 |
0.5 |
|
| 2007 |
Shao Q, Gao YQ. Asymmetry in kinesin walking. Biochemistry. 46: 9098-106. PMID 17630771 DOI: 10.1021/Bi602382W |
0.463 |
|
| 2006 |
Shao Q, Gao YQ. On the hand-over-hand mechanism of kinesin. Proceedings of the National Academy of Sciences of the United States of America. 103: 8072-7. PMID 16698919 DOI: 10.1073/Pnas.0602828103 |
0.455 |
|
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