☰

Jejoong Yoo, Ph.D. - Publications

Affiliations: 
2010 University of Wisconsin, Madison, Madison, WI 
Area:
computational chemistry and biophysics
Tree Info Similar researchers PubMed Report error

52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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
Show low-probability matches.