Year |
Citation |
Score |
2021 |
Kim M, Bae S, Oh I, Yoo J, Kim JS. Sequence-dependent twist-bend coupling in DNA minicircles. Nanoscale. PMID 34847218 DOI: 10.1039/d1nr04672a |
0.461 |
|
2021 |
Yoo J, Park S, Maffeo C, Ha T, Aksimentiev A. DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles. Nucleic Acids Research. PMID 34718725 DOI: 10.1093/nar/gkab967 |
0.646 |
|
2021 |
Bae S, Oh I, Yoo J, Kim JS. Effect of DNA Flexibility on Complex Formation of a Cationic Nanoparticle with Double-Stranded DNA. Acs Omega. 6: 18728-18736. PMID 34337212 DOI: 10.1021/acsomega.1c01709 |
0.379 |
|
2020 |
Yoo J, Winogradoff D, Aksimentiev A. Molecular dynamics simulations of DNA-DNA and DNA-protein interactions. Current Opinion in Structural Biology. 64: 88-96. PMID 32682257 DOI: 10.1016/J.Sbi.2020.06.007 |
0.658 |
|
2020 |
You S, Lee H, Kim K, Yoo J. Improved Parameterization of Protein-DNA Interactions for Molecular Dynamics Simulations of PCNA Diffusion on DNA. Journal of Chemical Theory and Computation. PMID 32543861 DOI: 10.1021/Acs.Jctc.0C00241 |
0.376 |
|
2019 |
You S, Yoo J. Molecular Dynamics Simulations using Accurate Charge-Charge Interactions Predict Unexpected Phase Behaviors of DNA Controlled by Epigenetic Modifications Biophysical Journal. 116: 437a. DOI: 10.1016/j.bpj.2018.11.2355 |
0.304 |
|
2018 |
Yoo J, Li CY, Slone SM, Maffeo C, Aksimentiev A. Correction to: A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems. Methods in Molecular Biology (Clifton, N.J.). 1811: E3. PMID 30484170 DOI: 10.1007/978-1-4939-8582-1_23 |
0.667 |
|
2018 |
Kang H, Yoo J, Sohn BK, Lee SW, Lee HS, Ma W, Kee JM, Aksimentiev A, Kim H. Sequence-dependent DNA condensation as a driving force of DNA phase separation. Nucleic Acids Research. PMID 30032232 DOI: 10.1093/Nar/Gky639 |
0.678 |
|
2018 |
Ohmann A, Li CY, Maffeo C, Al Nahas K, Baumann KN, Göpfrich K, Yoo J, Keyser UF, Aksimentiev A. A synthetic enzyme built from DNA flips 10 lipids per second in biological membranes. Nature Communications. 9: 2426. PMID 29930243 DOI: 10.1038/S41467-018-04821-5 |
0.655 |
|
2018 |
Yoo J, Li CY, Slone SM, Maffeo C, Aksimentiev A. A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems. Methods in Molecular Biology (Clifton, N.J.). 1811: 209-229. PMID 29926456 DOI: 10.1007/978-1-4939-8582-1_15 |
0.674 |
|
2018 |
Yoo J, Aksimentiev A. New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Physical Chemistry Chemical Physics : Pccp. PMID 29547221 DOI: 10.1039/C7Cp08185E |
0.613 |
|
2018 |
Ohmann A, Li C, Maffeo C, Al Nahas K, Baumann KN, Göpfrich K, Yoo J, Keyser UF, Aksimentiev A. Outperforming Nature: Synthetic Enzyme Built from DNA Flips Lipids of Biological Membranes at Record Rates Biophysical Journal. 114: 15a. DOI: 10.1016/J.Bpj.2017.11.128 |
0.624 |
|
2017 |
Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF. Correction to Ion Channels Made from a Single Membrane-Spanning DNA Duplex. Nano Letters. PMID 28608698 DOI: 10.1021/Acs.Nanolett.7B02430 |
0.642 |
|
2017 |
Yoo J, Park S, Kim H, Ha T, Aksimentiev A. High Throughput Simulations Reveal how Sequence and Methylation Control DNA Looping and Self-Association Biophysical Journal. 112: 6a. DOI: 10.1016/J.Bpj.2016.11.053 |
0.672 |
|
2016 |
Yoo J, Aksimentiev A. Refined Parameterization of Non-Bonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations. The Journal of Physical Chemistry Letters. PMID 27617340 DOI: 10.1021/Acs.Jpclett.6B01747 |
0.565 |
|
2016 |
Göpfrich K, Li CY, Ricci M, Bhamidimarri SP, Yoo J, Gyenes B, Ohmann A, Winterhalter M, Aksimentiev A, Keyser UF. Large-Conductance Transmembrane Porin Made from DNA Origami. Acs Nano. PMID 27504755 DOI: 10.1021/Acsnano.6B03759 |
0.701 |
|
2016 |
Göpfrich K, Li CY, Mames I, Bhamidimarri SP, Ricci M, Yoo J, Mames A, Ohmann A, Winterhalter M, Stulz E, Aksimentiev A, Keyser UF. Ion channels made from a single membrane-spanning DNA duplex. Nano Letters. PMID 27324157 DOI: 10.1021/Acs.Nanolett.6B02039 |
0.65 |
|
2016 |
Ko HG, Kim JI, Sim SE, Kim T, Yoo J, Choi SL, Baek SH, Yu WJ, Yoon JB, Sacktor TC, Kaang BK. The role of nuclear PKMζ in memory maintenance. Neurobiology of Learning and Memory. PMID 27321162 DOI: 10.1016/J.Nlm.2016.06.010 |
0.075 |
|
2016 |
Yoo J, Wilson J, Aksimentiev A. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields. Biopolymers. PMID 27144470 DOI: 10.1002/Bip.22868 |
0.638 |
|
2016 |
Bhattacharya S, Yoo J, Aksimentiev A. Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore. Acs Nano. PMID 27054820 DOI: 10.1021/Acsnano.6B00940 |
0.681 |
|
2016 |
Yoo J, Kim H, Aksimentiev A, Ha T. Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation. Nature Communications. 7: 11045. PMID 27001929 DOI: 10.1038/Ncomms11045 |
0.682 |
|
2016 |
Maffeo C, Yoo J, Aksimentiev A. De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation. Nucleic Acids Research. PMID 26980283 DOI: 10.1093/Nar/Gkw155 |
0.666 |
|
2016 |
Yu NK, Kim HF, Shim J, Kim S, Kim DW, Kwak C, Sim SE, Choi JH, Ahn S, Yoo J, Choi SL, Jang DJ, Lim CS, Lee YS, Kang C, et al. A transducible nuclear/nucleolar protein, mLLP, regulates neuronal morphogenesis and synaptic transmission. Scientific Reports. 6: 22892. PMID 26961175 DOI: 10.1038/Srep22892 |
0.074 |
|
2016 |
Ngo TT, Yoo J, Dai Q, Zhang Q, He C, Aksimentiev A, Ha T. Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. Nature Communications. 7: 10813. PMID 26905257 DOI: 10.1038/Ncomms10813 |
0.678 |
|
2016 |
Yoo J, Aksimentiev A. The structure and intermolecular forces of DNA condensates. Nucleic Acids Research. PMID 26883635 DOI: 10.1093/Nar/Gkw081 |
0.7 |
|
2016 |
Kim S, Kim T, Lee HR, Jang EH, Ryu HH, Kang M, Rah SY, Yoo J, Lee B, Kim JI, Lim CS, Kim SJ, Kim UH, Lee YS, Kaang BK. Impaired learning and memory in CD38 null mutant mice. Molecular Brain. 9: 16. PMID 26856703 DOI: 10.1186/S13041-016-0195-5 |
0.018 |
|
2016 |
Slone SM, Li CY, Yoo J, Aksimentiev A. Molecular mechanics of DNA bricks: In situ structure, mechanical properties and ionic conductivity New Journal of Physics. 18. DOI: 10.1088/1367-2630/18/5/055012 |
0.685 |
|
2016 |
Yoo J, Aksimentiev A. Improved Parameterization of Amine-Carboxyate, Amine-Phosphate, and Aliphatic Carbon-Carbon Interactions for Molecular Dynamics Simulations using the Charmm and Amber Force Fields Biophysical Journal. 110: 646a. DOI: 10.1016/J.Bpj.2015.11.3457 |
0.629 |
|
2016 |
Yoo J, Kim H, Ha T, Aksimentiev A. Effector-Free Molecular Mechanism of Epigenetic Regulation Revealed by Molecular Dynamics Simulations and Single-Molecule FRET Experiments Biophysical Journal. 110: 561a-562a. DOI: 10.1016/J.Bpj.2015.11.3003 |
0.664 |
|
2015 |
Yoo J, Aksimentiev A. Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields. Journal of Chemical Theory and Computation. PMID 26632962 DOI: 10.1021/Acs.Jctc.5B00967 |
0.611 |
|
2015 |
Yoo J, Aksimentiev A. Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport and Mechanical Gating. The Journal of Physical Chemistry Letters. PMID 26551518 DOI: 10.1021/Acs.Jpclett.5B01964 |
0.672 |
|
2015 |
Li CY, Hemmig EA, Kong J, Yoo J, Hernández-Ainsa S, Keyser UF, Aksimentiev A. Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field. Acs Nano. 9: 1420-33. PMID 25623807 DOI: 10.1021/Nn505825Z |
0.678 |
|
2014 |
Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A. Close encounters with DNA. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 26: 413101. PMID 25238560 DOI: 10.1088/0953-8984/26/41/413101 |
0.674 |
|
2014 |
Yoo J, Aksimentiev A. The Physics of DNA in Confinement Biophysical Journal. 106: 76a. DOI: 10.1016/J.Bpj.2013.11.496 |
0.707 |
|
2014 |
Kim H, Yoo J, Aksimentiev A, Ha T. ‘At’ Content as a Determinant of the Chromosome Structure Biophysical Journal. 106: 694a. DOI: 10.1016/J.Bpj.2013.11.3840 |
0.643 |
|
2014 |
Li C, Yoo J, Aksimentiev A. Ion Conductivity, Structural Dynamics and the Effective Force in DNA Origami Nanopores Biophysical Journal. 106: 414a. DOI: 10.1016/J.Bpj.2013.11.2331 |
0.717 |
|
2013 |
Yoo J, Aksimentiev A. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 110: 20099-104. PMID 24277840 DOI: 10.1073/Pnas.1316521110 |
0.686 |
|
2013 |
Yoo J, Jackson MB, Cui Q. A comparison of coarse-grained and continuum models for membrane bending in lipid bilayer fusion pores. Biophysical Journal. 104: 841-52. PMID 23442963 DOI: 10.1016/J.Bpj.2012.12.043 |
0.505 |
|
2013 |
Yoo J, Cui Q. Membrane-mediated protein-protein interactions and connection to elastic models: a coarse-grained simulation analysis of gramicidin A association. Biophysical Journal. 104: 128-38. PMID 23332065 DOI: 10.1016/J.Bpj.2012.11.3813 |
0.504 |
|
2013 |
Yoo J, Cui Q. Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A. Biophysical Journal. 104: 117-27. PMID 23332064 DOI: 10.1016/J.Bpj.2012.11.3812 |
0.509 |
|
2012 |
Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chemical Reviews. 112: 6250-84. PMID 23035940 DOI: 10.1021/Cr3002609 |
0.563 |
|
2012 |
Yoo J, Aksimentiev A. Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations. The Journal of Physical Chemistry. B. 116: 12946-54. PMID 23016894 DOI: 10.1021/Jp306598Y |
0.654 |
|
2012 |
Yoo J, Aksimentiev A. Improved parametrization of Li +, Na +, K +, and Mg 2+ ions for all-atom molecular dynamics simulations of nucleic acid systems Journal of Physical Chemistry Letters. 3: 45-50. DOI: 10.1021/Jz201501A |
0.688 |
|
2012 |
Yoo J, Aksimentiev A. Improved Parametrization of Ion-DNA Interactions for MD Simulations of Dense DNA Systems Biophysical Journal. 102: 637a. DOI: 10.1016/J.Bpj.2011.11.3468 |
0.684 |
|
2010 |
Yoo J, Cui Q. Chemical versus mechanical perturbations on the protonation state of arginine in complex lipid membranes: insights from microscopic pKa calculations. Biophysical Journal. 99: 1529-38. PMID 20816065 DOI: 10.1016/J.Bpj.2010.06.048 |
0.53 |
|
2009 |
Tang Y, Chen X, Yoo J, Yethiraj A, Cui Q. NUMERICAL SIMULATION OF NANOINDENTATION AND PATCH CLAMP EXPERIMENTS ON MECHANOSENSITIVE CHANNELS OF LARGE CONDUCTANCE IN ESCHERICHIA COLI. Shi Yan Li Xue = Journal of Experimental Mechanics / Zhongguo Li Xue Xue Hui, Zhongguo Ke Xue Ji Shu Da Xue Zhu Ban. 49: 35-46. PMID 21874098 DOI: 10.1007/S11340-007-9060-X |
0.541 |
|
2009 |
Yoo J, Cui Q. Curvature generation and pressure profile modulation in membrane by lysolipids: insights from coarse-grained simulations. Biophysical Journal. 97: 2267-76. PMID 19843459 DOI: 10.1016/J.Bpj.2009.07.051 |
0.531 |
|
2008 |
Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Mechanosensitive channels: insights from continuum-based simulations. Cell Biochemistry and Biophysics. 52: 1-18. PMID 18787764 DOI: 10.1007/S12013-008-9024-5 |
0.5 |
|
2008 |
Chen X, Cui Q, Tang Y, Yoo J, Yethiraj A. Gating mechanisms of mechanosensitive channels of large conductance, I: a continuum mechanics-based hierarchical framework. Biophysical Journal. 95: 563-80. PMID 18390626 DOI: 10.1529/Biophysj.107.128488 |
0.549 |
|
2008 |
Tang Y, Yoo J, Yethiraj A, Cui Q, Chen X. Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions. Biophysical Journal. 95: 581-96. PMID 18390625 DOI: 10.1529/Biophysj.107.128496 |
0.54 |
|
2008 |
Yoo J, Cui Q. Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations. Biophysical Journal. 94: L61-3. PMID 18199662 DOI: 10.1529/Biophysj.107.122945 |
0.516 |
|
2006 |
Tang Y, Cao G, Chen X, Yoo J, Yethiraj A, Cui Q. A finite element framework for studying the mechanical response of macromolecules: application to the gating of the mechanosensitive channel MscL. Biophysical Journal. 91: 1248-63. PMID 16731564 DOI: 10.1529/Biophysj.106.085985 |
0.555 |
|
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