Jejoong Yoo, Ph.D. - Publications

Affiliations: 
2010 University of Wisconsin, Madison, Madison, WI 
Area:
computational chemistry and biophysics

35 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
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2016 Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, Brandstetter J, Brondolin E, Dragicevic M, Erö J, Flechl M, Friedl M, Frühwirth R, Ghete VM, Hartl C, ... ... Yoo J, et al. Search for Narrow Resonances in Dijet Final States at sqrt[s]=8  TeV with the Novel CMS Technique of Data Scouting. Physical Review Letters. 117: 031802. PMID 27472109 DOI: 10.1103/PhysRevLett.117.031802  1
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  1
2016 Harmoko R, Yoo JY, Ko KS, Ramasamy NK, Hwang BY, Lee EJ, Kim HS, Lee KJ, Oh DB, Kim DY, Lee S, Li Y, Lee SY, Lee KO. N-glycan containing a core α1,3-fucose residue is required for basipetal auxin transport and gravitropic response in rice (Oryza sativa). The New Phytologist. PMID 27241276 DOI: 10.1111/nph.14031  1
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  1
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  1
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  1
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  1
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  1
2016 Yoo J, Aksimentiev A. The structure and intermolecular forces of DNA condensates. Nucleic Acids Research. PMID 26883635 DOI: 10.1093/nar/gkw081  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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