Year |
Citation |
Score |
2023 |
Zhang J, Liu S, Chen M, Chu H, Wang M, Wang Z, Yu J, Ni N, Yu F, Chen D, Yang YI, Xue B, Yang L, Liu Y, Gao YQ. Unsupervisedly Prompting AlphaFold2 for Accurate Few-Shot Protein Structure Prediction. Journal of Chemical Theory and Computation. PMID 37947474 DOI: 10.1021/acs.jctc.3c00528 |
0.439 |
|
2023 |
Zhang J, Chen D, Xia Y, Huang YP, Lin X, Han X, Ni N, Wang Z, Yu F, Yang L, Yang YI, Gao YQ. Artificial Intelligence Enhanced Molecular Simulations. Journal of Chemical Theory and Computation. PMID 37358079 DOI: 10.1021/acs.jctc.3c00214 |
0.455 |
|
2022 |
Lei YK, Zhang Z, Han X, Yang YI, Zhang J, Gao YQ. Locating Transition Zone in Phase Space. Journal of Chemical Theory and Computation. PMID 36135927 DOI: 10.1021/acs.jctc.2c00385 |
0.465 |
|
2022 |
Li M, Zhang J, Niu H, Lei YK, Han X, Yang L, Ye Z, Yang YI, Gao YQ. Phase Transition between Crystalline Variants of Ordinary Ice. The Journal of Physical Chemistry Letters. 13: 8601-8606. PMID 36073968 DOI: 10.1021/acs.jpclett.2c02176 |
0.475 |
|
2022 |
Han X, Zhang J, Yang YI, Zhang Z, Yang L, Gao YQ. Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels-Alder Reaction. Journal of Chemical Theory and Computation. PMID 35666128 DOI: 10.1021/acs.jctc.2c00233 |
0.514 |
|
2021 |
Zhang J, Lei YK, Zhang Z, Han X, Li M, Yang L, Yang YI, Gao YQ. Deep reinforcement learning of transition states. Physical Chemistry Chemical Physics : Pccp. PMID 33729229 DOI: 10.1039/d0cp06184k |
0.47 |
|
2020 |
Zhang J, Lei YK, Yang YI, Gao YQ. Deep learning for variational multiscale molecular modeling. The Journal of Chemical Physics. 153: 174115. PMID 33167648 DOI: 10.1063/5.0026836 |
0.466 |
|
2020 |
Zhang J, Lei YK, Zhang Z, Chang J, Li M, Han X, Yang L, Yang YI, Gao YQ. A Perspective on Deep Learning for Molecular Modeling and Simulations. The Journal of Physical Chemistry. A. PMID 32786668 DOI: 10.1021/acs.jpca.0c04473 |
0.438 |
|
2020 |
Zhang J, Lei YK, Zhang Z, Chang J, Li M, Han X, Yang L, Yang YI, Gao YQ. A Perspective on Deep Learning for Molecular Modeling and Simulations. The Journal of Physical Chemistry. B. PMID 32663004 DOI: 10.1021/acs.jpcb.0c04473 |
0.438 |
|
2020 |
Su QP, Zhao ZW, Meng L, Ding M, Zhang W, Li Y, Liu M, Li R, Gao YQ, Xie XS, Sun Y. Superresolution imaging reveals spatiotemporal propagation of human replication foci mediated by CTCF-organized chromatin structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 32541019 DOI: 10.1073/pnas.2001521117 |
0.533 |
|
2019 |
Zhang J, Lei YK, Che X, Zhang Z, Yang YI, Gao YQ. Deep Representation Learning for Complex Free-Energy Landscapes. The Journal of Physical Chemistry Letters. 5571-5576. PMID 31476868 DOI: 10.1021/acs.jpclett.9b02012 |
0.448 |
|
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 |
0.596 |
|
2019 |
Qiao Z, Zhao Y, Gao YQ. Ice Nucleation of Confined Monolayer Water Conforms to Classical Nucleation Theory. The Journal of Physical Chemistry Letters. 3115-3121. PMID 31117689 DOI: 10.1021/Acs.Jpclett.9B01169 |
0.568 |
|
2019 |
Cai X, Xie WJ, Yang Y, Long Z, Zhang J, Qiao Z, Yang L, Gao YQ. Structure of water confined between two parallel graphene plates. The Journal of Chemical Physics. 150: 124703. PMID 30927866 DOI: 10.1063/1.5080788 |
0.561 |
|
2019 |
Qiao Z, Xie WJ, Cai X, Gao YQ. Interlayer hopping dynamics of bilayer water confined between graphene sheets Chemical Physics Letters. 722: 153-159. DOI: 10.1016/J.Cplett.2019.02.046 |
0.563 |
|
2018 |
Liu S, Zhang L, Quan H, Tian H, Meng L, Yang L, Feng H, Gao YQ. From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective. Nucleic Acids Research. PMID 30053116 DOI: 10.1093/nar/gky633 |
0.531 |
|
2018 |
He Z, Feng G, Yang B, Yang L, Liu CW, Xu HG, Xu XL, Zheng WJ, Gao YQ. Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride. The Journal of Chemical Physics. 148: 222839. PMID 29907039 DOI: 10.1063/1.5024279 |
0.46 |
|
2017 |
Zhang L, Xie WJ, Liu S, Meng L, Gu C, Gao YQ. DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells. Biophysical Journal. 113: 1395-1404. PMID 28978434 DOI: 10.1016/j.bpj.2017.08.019 |
0.513 |
|
2017 |
Xie WJ, Meng L, Liu S, Zhang L, Cai X, Gao YQ. Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle. Scientific Reports. 7: 2818. PMID 28588240 DOI: 10.1038/s41598-017-02923-6 |
0.517 |
|
2017 |
Zhang J, Zhang Z, Yang YI, Liu S, Yang L, Gao YQ. Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories. Acs Central Science. 3: 407-414. PMID 28573202 DOI: 10.1021/acscentsci.7b00037 |
0.504 |
|
2016 |
Hou GL, Liu CW, Li RZ, Xu HG, Gao YQ, Zheng WJ. Emergence of Solvent-Separated Na(+)-Cl(-) Ion Pair in Salt Water: Photoelectron Spectroscopy and Theoretical Calculations. The Journal of Physical Chemistry Letters. 13-20. PMID 27935718 DOI: 10.1021/Acs.Jpclett.6B02670 |
0.434 |
|
2016 |
Fu J, Yang YI, Zhang J, Chen Q, Shen X, Gao YQ. Structural Characteristics of Homogeneous Hydrophobic Ionic Liquid-HNO3-H2O Ternary System: Experimental Studies and Molecular Dynamics Simulations. The Journal of Physical Chemistry. B. PMID 27196811 DOI: 10.1021/acs.jpcb.6b01214 |
0.488 |
|
2016 |
Yang YI, Zhang J, Che X, Yang L, Gao YQ. Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling. The Journal of Chemical Physics. 144: 094105. PMID 26957155 DOI: 10.1063/1.4943004 |
0.49 |
|
2016 |
Li X, Che X, Chen GH, Zhang J, Yan JL, Zhang YF, Zhang LS, Hsu CP, Gao YQ, Shi ZJ. Direct Oxidation of Aliphatic C-H Bonds in Amino-Containing Molecules under Transition-Metal-Free Conditions. Organic Letters. PMID 26949833 DOI: 10.1021/Acs.Orglett.5B03690 |
0.571 |
|
2016 |
Gao Y, Wu G, Ma F, Liu C, Jiang F, Wang Y, Wang A. Modified seeding method for preparing hierarchical nanocrystalline ZSM-5 catalysts for methanol aromatisation Microporous and Mesoporous Materials. 226: 251-259. DOI: 10.1016/j.micromeso.2015.11.066 |
0.329 |
|
2016 |
Gao Y, Hu Y, Ren P, Zhou D, Qiu J. Effect of Li+ ions on the enhancement upconversion and stokes emission of NaYF4:Tb, Yb co-doped in glass-ceramics Journal of Alloys and Compounds. 667: 297-301. DOI: 10.1016/j.jallcom.2016.01.200 |
0.356 |
|
2015 |
Xie WJ, Yang YI, Gao YQ. Dual reorientation relaxation routes of water molecules in oxyanion's hydration shell: A molecular geometry perspective. The Journal of Chemical Physics. 143: 224504. PMID 26671387 DOI: 10.1063/1.4937361 |
0.463 |
|
2015 |
Li RZ, Hou GL, Liu CW, Xu HG, Zhao X, Gao YQ, Zheng WJ. Initial hydration behavior of sodium iodide dimer: photoelectron spectroscopy and ab initio calculations. Physical Chemistry Chemical Physics : Pccp. PMID 26618327 DOI: 10.1039/C5Cp05550D |
0.418 |
|
2015 |
Zhang J, Yang YI, Yang L, Gao YQ. Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories. The Journal of Physical Chemistry. B. PMID 26485567 DOI: 10.1021/acs.jpcb.5b08690 |
0.517 |
|
2015 |
Gu C, Zhang J, Yang YI, Chen X, Ge H, Sun Y, Su X, Yang L, Xie XS, Gao YQ. DNA Structural Correlation in Short and Long Ranges. The Journal of Physical Chemistry. B. PMID 26439165 DOI: 10.1021/Acs.Jpcb.5B06217 |
0.454 |
|
2015 |
Zhang J, Yang YI, Yang L, Gao YQ. Conformational Preadjustment in Aqueous Claisen Rearrangement Revealed by SITS-QM/MM MD Simulations. The Journal of Physical Chemistry. B. 119: 5518-30. PMID 25849201 DOI: 10.1021/jp511057f |
0.527 |
|
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 |
0.612 |
|
2015 |
Zeng Z, Liu CW, Hou GL, Feng G, Xu HG, Gao YQ, Zheng WJ. Photoelectron spectroscopy and ab initio calculations of Li(H₂O)n(-) and Cs(H₂O)n(-) (n = 1-6) clusters. The Journal of Physical Chemistry. A. 119: 2845-56. PMID 25723570 DOI: 10.1021/Jp512177J |
0.427 |
|
2015 |
Yang YI, Gao YQ. Computer simulation studies of Aβ37-42 aggregation thermodynamics and kinetics in water and salt solution. The Journal of Physical Chemistry. B. 119: 662-70. PMID 24861904 DOI: 10.1021/jp502169b |
0.44 |
|
2015 |
Xiao H, Tang B, Liu C, Gao Y, Yu S, Jiang S. Dynamic precipitation in a Mg-Gd-Y-Zr alloy during hot compression Materials Science and Engineering A. 645: 241-247. DOI: 10.1016/j.msea.2015.08.022 |
0.344 |
|
2015 |
Liu CW, Gao YQ. Understanding the microsolvation of salts in molecular clusters International Journal of Quantum Chemistry. 115: 541-544. DOI: 10.1002/Qua.24827 |
0.439 |
|
2014 |
Liu CW, Wang F, Yang L, Li XZ, Zheng WJ, Gao YQ. Stable salt-water cluster structures reflect the delicate competition between ion-water and water-water interactions. The Journal of Physical Chemistry. B. 118: 743-51. PMID 24387307 DOI: 10.1021/Jp408439J |
0.435 |
|
2014 |
Liu CW, Hou GL, Zheng WJ, Gao YQ. Adsorption of water molecules on sodium chloride trimer Theoretical Chemistry Accounts. 133. DOI: 10.1007/S00214-014-1550-1 |
0.442 |
|
2013 |
Li RZ, Liu CW, Gao YQ, Jiang H, Xu HG, Zheng WJ. Microsolvation of LiI and CsI in water: anion photoelectron spectroscopy and ab initio calculations. Journal of the American Chemical Society. 135: 5190-9. PMID 23432353 DOI: 10.1021/Ja4006942 |
0.41 |
|
2013 |
Zhang Q, Xie W, Bian H, Gao YQ, Zheng J, Zhuang W. Microscopic origin of the deviation from Stokes-Einstein behavior observed in dynamics of the KSCN aqueous solutions: a MD simulation study. The Journal of Physical Chemistry. B. 117: 2992-3004. PMID 23414456 DOI: 10.1021/Jp400441E |
0.549 |
|
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 |
0.452 |
|
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 |
0.446 |
|
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 |
0.478 |
|
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 |
0.473 |
|
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 |
0.454 |
|
2012 |
Cao Q, Wang XJ, Liu CW, Liu DF, Li LF, Gao YQ, Su XD. Inhibitory mechanism of caspase-6 phosphorylation revealed by crystal structures, molecular dynamics simulations, and biochemical assays. The Journal of Biological Chemistry. 287: 15371-9. PMID 22433863 DOI: 10.1074/Jbc.M112.351213 |
0.394 |
|
2012 |
Yang L, Shao Q, Gao Y. Enhanced sampling method in molecular simulations Progress in Chemistry. 24: 1199-1213. |
0.441 |
|
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 |
0.472 |
|
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 |
0.494 |
|
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 |
0.497 |
|
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 |
0.454 |
|
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 |
0.464 |
|
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 |
0.443 |
|
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 |
0.48 |
|
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 |
0.426 |
|
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 |
0.489 |
|
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 |
0.462 |
|
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 |
0.454 |
|
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 |
0.501 |
|
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 |
0.454 |
|
2007 |
Gao YQ, Marcus RA. An approximate theory of the ozone isotopic effects: rate constant ratios and pressure dependence. The Journal of Chemical Physics. 127: 244316. PMID 18163684 DOI: 10.1063/1.2806189 |
0.559 |
|
2007 |
Shao Q, Gao YQ. Asymmetry in kinesin walking. Biochemistry. 46: 9098-106. PMID 17630771 DOI: 10.1021/Bi602382W |
0.425 |
|
2007 |
Wu Y, Gao YQ, Karplus M. A kinetic model of coordinated myosin V. Biochemistry. 46: 6318-30. PMID 17487986 DOI: 10.1021/Bi700526R |
0.347 |
|
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 |
0.418 |
|
2006 |
Gao YQ, Yang W, Karplus M. Thermodynamics and kinetic analysis of F0F1-ATPase Modern Methods For Theoretical Physical Chemistry of Biopolymers. 249-263. DOI: 10.1016/B978-044452220-7/50077-0 |
0.346 |
|
2005 |
Gao YQ, Yang W, Karplus M. A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell. 123: 195-205. PMID 16239139 DOI: 10.1016/J.Cell.2005.10.001 |
0.339 |
|
2005 |
Karplus M, Gao YQ, Ma J, van der Vaart A, Yang W. Protein structural transitions and their functional role. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 363: 331-55; discussion 3. PMID 15664887 DOI: 10.1098/Rsta.2004.1496 |
0.603 |
|
2004 |
Karplus M, Gao YQ. Biomolecular motors: the F1-ATPase paradigm. Current Opinion in Structural Biology. 14: 250-9. PMID 15093841 DOI: 10.1016/J.Sbi.2004.03.012 |
0.327 |
|
2003 |
Gao YQ, Yang W, Marcus RA, Karplus M. A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 100: 11339-44. PMID 14500780 DOI: 10.1073/Pnas.1334188100 |
0.619 |
|
2003 |
Yang W, Gao YQ, Cui Q, Ma J, Karplus M. The missing link between thermodynamics and structure in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America. 100: 874-9. PMID 12552084 DOI: 10.1073/Pnas.0337432100 |
0.486 |
|
2002 |
Gao YQ, Chen WC, Marcus RA. A theoretical study of ozone isotopic effects using a modified ab initio potential energy surface Journal of Chemical Physics. 117: 1536-1543. DOI: 10.1063/1.1488577 |
0.576 |
|
2002 |
Gao YQ, Marcus RA. Erratum: “On the theory of the strange and unconventional isotopic effects in ozone formation” [J. Chem. Phys. 116, 137 (2002)] The Journal of Chemical Physics. 116: 5913-5913. DOI: 10.1063/1.1458540 |
0.523 |
|
2002 |
Gao YQ, Marcus RA. On the theory of the strange and unconventional isotopic effects in ozone formation Journal of Chemical Physics. 116: 137-154. DOI: 10.1063/1.1415448 |
0.579 |
|
2002 |
Gao YQ, Marcus RA. Theoretical investigation of the directional electron transfer in 4-aminonaphthalimide compounds Journal of Physical Chemistry A. 106: 1956-1960. DOI: 10.1021/Jp011980S |
0.535 |
|
2001 |
Gao YQ, Marcus RA. Strange and unconventional isotope effects in ozone formation. Science (New York, N.Y.). 293: 259-63. PMID 11387441 DOI: 10.1126/Science.1058528 |
0.569 |
|
2001 |
Gao YQ, Marcus RA. Application of the z-transform to composite materials Journal of Chemical Physics. 115: 9929-9934. DOI: 10.1063/1.1416127 |
0.537 |
|
2001 |
Marcus RA, Gao YQ. Pressure effects on bimolecular recombination and unimolecular dissociation reactions Journal of Chemical Physics. 114: 9807-9812. DOI: 10.1063/1.1370552 |
0.562 |
|
2000 |
Gao YQ, Georgievskii Y, Marcus RA. On the theory of electron transfer reactions at semiconductor electrode/liquid interfaces Journal of Chemical Physics. 112: 3358-3369. DOI: 10.1063/1.480918 |
0.568 |
|
2000 |
Gao YQ, Marcus RA. On the theory of electron transfer reactions at semiconductor/liquid interfaces. II. A free electron model Journal of Chemical Physics. 113: 6351-6360. DOI: 10.1063/1.1309528 |
0.55 |
|
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