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Xu L, Chen LY. Association of sigma-1 receptor with dopamine transporter attenuates the binding of methamphetamine via distinct helix-helix interactions. Chem Biol Drug Des. 2021 Jun;97(6):1194-1209. doi: 10.1111/cbdd.13841. Epub 2021 Apr 4. PubMed PMID: 33754484; PubMed Central PMCID: PMC8113090.
Xu L, Chen LY. Molecular determinant of substrate binding and specificity of cytochrome P450 2J2. Sci Rep. 2020 Dec 17;10(1):22267. doi: 10.1038/s41598-020-79284-0. PubMed PMID: 33335233; PubMed Central PMCID: PMC7746748.
Rodriguez RA, Chan R, Liang H, Chen LY. Quantitative study of unsaturated transport of glycerol through aquaglyceroporin that has high affinity for glycerol. RSC Adv. 2020;10(56):34203-34214. doi: 10.1039/d0ra05262k. Epub 2020 Sep 15. PubMed PMID: 32944226; PubMed Central PMCID: PMC7494219.
Xu L, Chen LY. Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter. J Chem Inf Model. 2020 Aug 24;60(8):3958-3968. doi: 10.1021/acs.jcim.0c00346. Epub 2020 Jul 21. PubMed PMID: 32649824; PubMed Central PMCID: PMC7484383.
Chen LY. Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions. Front Phys. 2020 Jun;8. doi: 10.3389/fphy.2020.00202. Epub 2020 Jun 9. PubMed PMID: 32542181; PubMed Central PMCID: PMC7295167.
Chan R, Falato M, Liang H, Chen LY. In silico simulations of erythrocyte aquaporins with quantitative in vitro validation. RSC Adv. 2020;10(36):21283-21291. doi: 10.1039/d0ra03456h. Epub 2020 Jun 4. PubMed PMID: 32612811; PubMed Central PMCID: PMC7328926.
Chen LY. Application of the Brown dynamics fluctuation-dissipation theorem to the study of Plasmodium berghei transporter protein PbAQP. Front Phys. 2020 Apr;8. doi: 10.3389/fphy.2020.00119. Epub 2020 Apr 17. PubMed PMID: 32457897; PubMed Central PMCID: PMC7250396.
Chen LY, Phelix CF. Extracellular gating of glucose transport through GLUT 1. Biochem Biophys Res Commun. 2019 Apr 9;511(3):573-578. doi: 10.1016/j.bbrc.2019.02.067. Epub 2019 Feb 27. PubMed PMID: 30824189; PubMed Central PMCID: PMC6452493.
Rodriguez RA, Liang H, Chen LY, Plascencia-Villa G, Perry G. Single-channel permeability and glycerol affinity of human aquaglyceroporin AQP3. Biochim Biophys Acta Biomembr. 2019 Apr 1;1861(4):768-775. doi: 10.1016/j.bbamem.2019.01.008. Epub 2019 Jan 17. PubMed PMID: 30659792; PubMed Central PMCID: PMC6382548.
Chen LY. Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1. [preprint]. 2019; [revised 2020]: Available from: doi: 10.1101/787259.
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 Nov 21;9(11):2815-2823. doi: 10.1021/acschemneuro.8b00223. Epub 2018 Jun 11. PubMed PMID: 29865792; PubMed Central PMCID: PMC6256350.
Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Thermodynamics of Amyloid-β Fibril Elongation: Atomistic Details of the Transition State. ACS Chem Neurosci. 2018 Apr 18;9(4):783-789. doi: 10.1021/acschemneuro.7b00409. Epub 2017 Dec 27. PubMed PMID: 29239603; PubMed Central PMCID: PMC5911799.
Wambo TO, Chen LY, Phelix C, Perry G. Affinity and path of binding xylopyranose unto E. coli xylose permease. Biochem Biophys Res Commun. 2017 Dec 9;494(1-2):202-206. doi: 10.1016/j.bbrc.2017.10.053. Epub 2017 Oct 12. PubMed PMID: 29032199; PubMed Central PMCID: PMC5670004.
Wambo TO, Rodriguez RA, Chen LY. Computing osmotic permeabilities of aquaporins AQP4, AQP5, and GlpF from near-equilibrium simulations. Biochim Biophys Acta Biomembr. 2017 Aug;1859(8):1310-1316. doi: 10.1016/j.bbamem.2017.04.022. Epub 2017 Apr 25. PubMed PMID: 28455098; PubMed Central PMCID: PMC5493307.
Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Elongation affinity, activation barrier, and stability of Aβ42 oligomers/fibrils in physiological saline. Biochem Biophys Res Commun. 2017 May 27;487(2):444-449. doi: 10.1016/j.bbrc.2017.04.084. Epub 2017 Apr 17. PubMed PMID: 28427941; PubMed Central PMCID: PMC5489073.
Villarreal OD, Yu L, Rodriguez RA, Chen LY. Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. Biochem Biophys Res Commun. 2017 Jan 29;483(1):203-208. doi: 10.1016/j.bbrc.2016.12.165. Epub 2016 Dec 26. PubMed PMID: 28034750; PubMed Central PMCID: PMC5253313.
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 Jul-Aug;214-215:54-60. doi: 10.1016/j.bpc.2016.05.006. Epub 2016 May 18. PubMed PMID: 27232456; PubMed Central PMCID: PMC4901522.
Yu L, Rodriguez RA, Chen LL, Chen LY, Perry G, McHardy SF, Yeh CK. 1,3-propanediol binds deep inside the channel to inhibit water permeation through aquaporins. Protein Sci. 2016 Feb;25(2):433-41. doi: 10.1002/pro.2832. PubMed PMID: 26481430; PubMed Central PMCID: PMC4815352.
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(1):91-98. doi: 10.15761/jsin.1000117. Epub 2016 Jan 23. PubMed PMID: 27213050; PubMed Central PMCID: PMC4873003.
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 Dec 17;119(50):15502-8. doi: 10.1021/acs.jpcb.5b09864. Epub 2015 Dec 3. PubMed PMID: 26581232; PubMed Central PMCID: PMC4684460.
Rodriguez RA, Yu L, Chen LY. Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics. J Chem Theory Comput. 2015 Sep 8;11(9):4427-4438. doi: 10.1021/acs.jctc.5b00340. PubMed PMID: 26366131; PubMed Central PMCID: PMC4565455.
Chen LY. Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach. Mol Membr Biol. 2015;32(1):19-25. doi: 10.3109/09687688.2015.1006275. Epub 2015 May 8. PubMed PMID: 25955791; PubMed Central PMCID: PMC4523441.
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 Apr 14;11(4):1928-38. doi: 10.1021/ct501162f. PubMed PMID: 25937822; PubMed Central PMCID: PMC4411208.
Chen LY. Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin. Biophys Chem. 2015 Mar;198:14-21. doi: 10.1016/j.bpc.2015.01.004. Epub 2015 Jan 14. PubMed PMID: 25637890; PubMed Central PMCID: PMC4339505.
Villarreal OD, Chen LY, Whetten RL, Yacaman MJ. Ligand-modulated interactions between charged monolayer-protected Au144(SR)60 gold nanoparticles in physiological saline. Phys Chem Chem Phys. 2015 Feb 7;17(5):3680-8. doi: 10.1039/c4cp05137h. PubMed PMID: 25556346; PubMed Central PMCID: PMC4303505.
Chen LY. Does Plasmodium falciparum have an Achilles' heel?. Malar Chemother Control Elimin. 2014 Apr 5;3(1). doi: 10.4172/2090-2778.1000114. PubMed PMID: 25346857; PubMed Central PMCID: PMC4205581.
Alsharif SA, Chen LY, Tlahuice-Flores A, Whetten RL, Yacaman MJ. Interaction between functionalized gold nanoparticles in physiological saline. Phys Chem Chem Phys. 2014 Mar 7;16(9):3909-13. doi: 10.1039/c3cp54503b. PubMed PMID: 24441708; PubMed Central PMCID: PMC3947887.
Chen LY. Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF. Biochim Biophys Acta. 2013 Aug;1828(8):1786-93. doi: 10.1016/j.bbamem.2013.03.008. Epub 2013 Mar 16. PubMed PMID: 23506682; PubMed Central PMCID: PMC3761968.
Zhang YB, Chen LY. In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid. Biophys Chem. 2013 Jan;171:24-30. doi: 10.1016/j.bpc.2012.09.004. Epub 2012 Oct 2. PubMed PMID: 23176748; PubMed Central PMCID: PMC3546230.
Chen LY. Glycerol inhibits water permeation through Plasmodium falciparum aquaglyceroporin. J Struct Biol. 2013 Jan;181(1):71-6. doi: 10.1016/j.jsb.2012.10.007. Epub 2012 Oct 26. PubMed PMID: 23108237; PubMed Central PMCID: PMC3525719.
Hu G, Chen LY, Wang J. Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z. J Mol Model. 2012 Aug;18(8):3731-41. doi: 10.1007/s00894-012-1379-2. Epub 2012 Mar 6. PubMed PMID: 22392432; PubMed Central PMCID: PMC3809118.
Zhang Y, Cui Y, Chen LY. Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel. Biophys Chem. 2012 Jan;160(1):69-74. doi: 10.1016/j.bpc.2011.07.006. Epub 2011 Aug 3. PubMed PMID: 21963041; PubMed Central PMCID: PMC3210408.
Renthal R, Brancaleon L, Peña I, Silva F, Chen LY. Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles. Biophys Chem. 2011 Dec;159(2-3):321-7. doi: 10.1016/j.bpc.2011.08.005. Epub 2011 Aug 27. PubMed PMID: 21924540; PubMed Central PMCID: PMC3192009.
Ikonen T, Khandkar MD, Chen LY, Ying SC, Ala-Nissila T. Diffusion in periodic potentials with path integral hyperdynamics. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Aug;84(2 Pt 2):026703. doi: 10.1103/PhysRevE.84.026703. Epub 2011 Aug 5. PubMed PMID: 21929140; PubMed Central PMCID: PMC3177431.
Hu G, Zhang Q, Chen LY. Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation. J Mol Model. 2011 Aug;17(8):1919-26. doi: 10.1007/s00894-010-0892-4. Epub 2010 Nov 26. PubMed PMID: 21110054; PubMed Central PMCID: PMC3144287.
Chen LY. Exploring the free-energy landscapes of biological systems with steered molecular dynamics. Phys Chem Chem Phys. 2011 Apr 7;13(13):6176-83. doi: 10.1039/c0cp02799e. Epub 2011 Feb 25. PubMed PMID: 21359274; PubMed Central PMCID: PMC3111135.
Hu G, Chen LY. In silico experiments of single-chain antibody fragment against drugs of abuse. Biophys Chem. 2010 Dec;153(1):97-103. doi: 10.1016/j.bpc.2010.10.008. Epub 2010 Oct 18. PubMed PMID: 21056529; PubMed Central PMCID: PMC3006299.
Chen LY. Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations. Biophys Chem. 2010 Oct;151(3):178-80. doi: 10.1016/j.bpc.2010.05.014. Epub 2010 Jun 11. PubMed PMID: 20573441; PubMed Central PMCID: PMC2926166.
Chen LY, Bastien DA, Espejel HE. Determination of equilibrium free energy from nonequilibrium work measurements. Phys Chem Chem Phys. 2010 Jul 7;12(25):6579-82. doi: 10.1039/b926889h. Epub 2010 May 12. PubMed PMID: 20463999; PubMed Central PMCID: PMC2888695.
Chen LY. Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics. J Chem Phys. 2008 Oct 14;129(14):144113. doi: 10.1063/1.2992153. PubMed PMID: 19045140; PubMed Central PMCID: PMC2671654.
Chen LY. On the Crooks fluctuation theorem and the Jarzynski equality. J Chem Phys. 2008 Sep 7;129(9):091101. doi: 10.1063/1.2978949. PubMed PMID: 19044857; PubMed Central PMCID: PMC2671671.
Chen LY, Horing NJ. Study of Lennard-Jones clusters: Effects of anharmonicities far from saddle points. International Journal of High Speed Electronics and Systems. 2008; 18:119.
Chen LY, Horing NJ. An exact formulation of hyperdynamics simulations. J Chem Phys. 2007 Jun 14;126(22):224103. doi: 10.1063/1.2737454. PubMed PMID: 17581040; PubMed Central PMCID: PMC3770272.
Horing NJ, Chen LY, Cui HL. Dielectric Response of a Planar Periodic Array of Polarizable Wires Parallel to an Interface with a Nonlocal Dynamic Plasma-like Medium. Physics Letters A. 2007; 361:164. doi: 10.1016/j.physleta.2006.09.037.
Horing N, Chen L. Inverse dielectric function of a lateral quantum wire superlattice parallel to the interface of a plasma-like semiconductor. Physical Review B. 2006 November; 74(19):-. doi: 10.1103/PhysRevB.74.195336.
Chen LY, Horing NJ. Transition rate prefactors for systems of many degrees of freedom. J Chem Phys. 2006 Apr 28;124(16):164102. doi: 10.1063/1.2188943. PubMed PMID: 16674124; NIHMSID:NIHMS212720.
Horing NJ, Chen LY. Inverse Dielectric Function of a Lateral Quantum Wire Superlattice Parallel to the Interface of a Plasma-Like Semiconductor. Physical Review B. 2006; 74:195336.
Nash PL, Chen LY. Factorization of the constants of the motion. Canadian Journal of Physics. 2006; 84:717.
Chen LY, Nash PL, Horing NJ. Efficient transition path sampling for systems with multiple reaction pathways. J Chem Phys. 2005 Sep 1;123(9):94104. doi: 10.1063/1.2013213. PubMed PMID: 16164338; NIHMSID:NIHMS212719.
Chen LY, Nash PL. Path integral approach to Brownian motion driven with an ac force. J Chem Phys. 2004 Sep 1;121(9):3984-8. doi: 10.1063/1.1776115. PubMed PMID: 15332944; NIHMSID:NIHMS212718.
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