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For: Chen LY. Exploring the free-energy landscapes of biological systems with steered molecular dynamics. Phys Chem Chem Phys 2011;13:6176-83. [PMID: 21359274 DOI: 10.1039/c0cp02799e] [Cited by in Crossref: 24] [Cited by in F6Publishing: 22] [Article Influence: 2.2] [Reference Citation Analysis]
Number Citing Articles
1 Wan H, Hu J, Tian X, Chang S. Molecular dynamics simulations of wild type and mutants of human complement receptor 2 complexed with C3d. Phys Chem Chem Phys 2013;15:1241-51. [DOI: 10.1039/c2cp41388d] [Cited by in Crossref: 42] [Cited by in F6Publishing: 12] [Article Influence: 4.7] [Reference Citation Analysis]
2 Yang Z, Wei T, Huang H, Yang H, Zhou Y, Xu D. Insights into the biotransformation of 2,4,6-trinitrotoluene by the old yellow enzyme family of flavoproteins. A computational study. Phys Chem Chem Phys 2019;21:11589-98. [PMID: 30801593 DOI: 10.1039/c8cp07873d] [Cited by in Crossref: 3] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
3 Siders PD. Conformational free energy of alkylsilanes by nonequilibrium-pulling Monte Carlo simulation. Molecular Simulation 2015;42:693-701. [DOI: 10.1080/08927022.2015.1083101] [Cited by in Crossref: 6] [Cited by in F6Publishing: 3] [Article Influence: 0.9] [Reference Citation Analysis]
4 Hu G, Xu S, Wang J. Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations. Chem Biol Drug Des 2015;86:1351-9. [PMID: 26032728 DOI: 10.1111/cbdd.12598] [Cited by in Crossref: 17] [Cited by in F6Publishing: 16] [Article Influence: 2.4] [Reference Citation Analysis]
5 Chen LY. Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach. Mol Membr Biol 2015;32:19-25. [PMID: 25955791 DOI: 10.3109/09687688.2015.1006275] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 0.6] [Reference Citation Analysis]
6 Chen LY. Glycerol inhibits water permeation through Plasmodium falciparum aquaglyceroporin. J Struct Biol 2013;181:71-6. [PMID: 23108237 DOI: 10.1016/j.jsb.2012.10.007] [Cited by in Crossref: 10] [Cited by in F6Publishing: 10] [Article Influence: 1.0] [Reference Citation Analysis]
7 Hu G, Cao Z, Xu S, Wang W, Wang J. Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods. Sci Rep 2015;5:16481. [PMID: 26568041 DOI: 10.1038/srep16481] [Cited by in Crossref: 19] [Cited by in F6Publishing: 17] [Article Influence: 2.7] [Reference Citation Analysis]
8 Chen LY. Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin. Biophys Chem 2015;198:14-21. [PMID: 25637890 DOI: 10.1016/j.bpc.2015.01.004] [Cited by in Crossref: 6] [Cited by in F6Publishing: 6] [Article Influence: 0.9] [Reference Citation Analysis]
9 Chen LY. Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF. Biochim Biophys Acta 2013;1828:1786-93. [PMID: 23506682 DOI: 10.1016/j.bbamem.2013.03.008] [Cited by in Crossref: 22] [Cited by in F6Publishing: 23] [Article Influence: 2.4] [Reference Citation Analysis]
10 Zhang Y, Cui Y, Chen LY. Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel. Biophys Chem 2012;160:69-74. [PMID: 21963041 DOI: 10.1016/j.bpc.2011.07.006] [Cited by in Crossref: 16] [Cited by in F6Publishing: 15] [Article Influence: 1.5] [Reference Citation Analysis]
11 Wambo TO, Chen LY, McHardy SF, Tsin AT. Molecular dynamics study of human carbonic anhydrase II in complex with Zn(2+) and acetazolamide on the basis of all-atom force field simulations. Biophys Chem 2016;214-215:54-60. [PMID: 27232456 DOI: 10.1016/j.bpc.2016.05.006] [Cited by in Crossref: 9] [Cited by in F6Publishing: 9] [Article Influence: 1.5] [Reference Citation Analysis]
12 Liang H, Bourdon AK, Chen LY, Phelix CF, Perry G. Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3. ACS Chem Neurosci 2018;9:2815-23. [PMID: 29865792 DOI: 10.1021/acschemneuro.8b00223] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 1.0] [Reference Citation Analysis]
13 Yu L, Villarreal OD, Chen LL, Chen LY. 1,3-Propanediol binds inside the water-conducting pore of aquaporin 4: Does this efficacious inhibitor have sufficient potency? J Syst Integr Neurosci 2016;2:91-8. [PMID: 27213050 DOI: 10.15761/jsin.1000117] [Cited by in Crossref: 6] [Cited by in F6Publishing: 5] [Article Influence: 1.0] [Reference Citation Analysis]
14 Rodriguez RA, Yu L, Chen LY. Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics. J Chem Theory Comput 2015;11:4427-38. [PMID: 26366131 DOI: 10.1021/acs.jctc.5b00340] [Cited by in Crossref: 26] [Cited by in F6Publishing: 20] [Article Influence: 4.3] [Reference Citation Analysis]
15 Yang Z, Chen J, Zhou Y, Huang H, Xu D, Zhang C. Understanding the hydrogen transfer mechanism for the biodegradation of 2,4,6-trinitrotoluene catalyzed by pentaerythritol tetranitrate reductase: molecular dynamics simulations. Phys Chem Chem Phys 2018;20:12157-65. [DOI: 10.1039/c8cp00345a] [Cited by in Crossref: 9] [Cited by in F6Publishing: 1] [Article Influence: 2.3] [Reference Citation Analysis]
16 Hu G, Chen LY, Wang J. Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z. J Mol Model 2012;18:3731-41. [PMID: 22392432 DOI: 10.1007/s00894-012-1379-2] [Cited by in Crossref: 10] [Cited by in F6Publishing: 9] [Article Influence: 1.0] [Reference Citation Analysis]
17 Villarreal OD, Chen LY, Whetten RL, Demeler B. Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles. J Phys Chem B 2015;119:15502-8. [PMID: 26581232 DOI: 10.1021/acs.jpcb.5b09864] [Cited by in Crossref: 6] [Article Influence: 0.9] [Reference Citation Analysis]
18 Patel JS, Branduardi D, Masetti M, Rocchia W, Cavalli A. Insights into Ligand-Protein Binding from Local Mechanical Response. J Chem Theory Comput 2011;7:3368-78. [PMID: 22003321 DOI: 10.1021/ct200324j] [Cited by in Crossref: 13] [Cited by in F6Publishing: 13] [Article Influence: 1.2] [Reference Citation Analysis]
19 Alsharif SA, Chen LY, Tlahuice-Flores A, Whetten RL, Yacaman MJ. Interaction between functionalized gold nanoparticles in physiological saline. Phys Chem Chem Phys 2014;16:3909-13. [PMID: 24441708 DOI: 10.1039/c3cp54503b] [Cited by in Crossref: 17] [Cited by in F6Publishing: 13] [Article Influence: 2.1] [Reference Citation Analysis]
20 Holland BW, Gray CG, Tomberli B. Calculating diffusion and permeability coefficients with the oscillating forward-reverse method. Phys Rev E 2012;86. [DOI: 10.1103/physreve.86.036707] [Cited by in Crossref: 14] [Cited by in F6Publishing: 6] [Article Influence: 1.4] [Reference Citation Analysis]
21 Jeřábek P, Florián J, Stiborová M, Martínek V. Flexible docking-based molecular dynamics/steered molecular dynamics calculations of protein-protein contacts in a complex of cytochrome P450 1A2 with cytochrome b5. Biochemistry 2014;53:6695-705. [PMID: 25313797 DOI: 10.1021/bi500814t] [Cited by in Crossref: 15] [Cited by in F6Publishing: 12] [Article Influence: 1.9] [Reference Citation Analysis]
22 Schäfer K, Oestereich M, Gauss J, Diezemann G. Force probe simulations using a hybrid scheme with virtual sites. J Chem Phys 2017;147:134909. [PMID: 28987102 DOI: 10.1063/1.4986194] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 0.4] [Reference Citation Analysis]
23 Chen LY. Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate. J Chem Theory Comput 2015;11:1928-38. [PMID: 25937822 DOI: 10.1021/ct501162f] [Cited by in Crossref: 26] [Cited by in F6Publishing: 24] [Article Influence: 4.3] [Reference Citation Analysis]
24 Knoch F, Schäfer K, Diezemann G, Speck T. Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding. J Chem Phys 2018;148:044109. [PMID: 29390802 DOI: 10.1063/1.5010435] [Cited by in Crossref: 5] [Cited by in F6Publishing: 3] [Article Influence: 1.3] [Reference Citation Analysis]