Sunhwan Jo, Ph.D. - Publications

2013 Molecular Biosciences University of Kansas, Lawrence, KS, United States 

58 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
2020 Takimoto T, Sasaki H, Tsue H, Takahashi H, MacKerell AD, Nakano K, Okazaki E, Nakamura A, Betsuyaku T, Tachibana R, Hioki K, Yoluk O, Jo S. Simple Synthesis of a Heterocyclophane Exhibiting Anti-c-Met Activity by Acting as a Hatch Blocking Access to the Active Site. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 33258147 DOI: 10.1002/chem.202001382  0.44
2020 Somani S, Jo S, Thirumangalathu R, Rodrigues D, Tanenbaum LM, Amin K, MacKerell AD, Thakkar SV. Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS). Journal of Pharmaceutical Sciences. PMID 33137372 DOI: 10.1016/j.xphs.2020.10.051  0.44
2020 Jo S, Xu A, Curtis JE, Somani S, MacKerell AD. Computational Characterization of Antibody-Excipient Interactions for Rational Excipient Selection using the Site Identification by Ligand Competitive Saturation (SILCS)-Biologics Approach. Molecular Pharmaceutics. PMID 32965126 DOI: 10.1021/acs.molpharmaceut.0c00775  0.44
2020 MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochimica Et Biophysica Acta. General Subjects. 129519. PMID 31911242 DOI: 10.1016/J.Bbagen.2020.129519  0.44
2019 Suh D, Jo S, Jiang W, Chipot C, Roux B. String method for Protein-Protein Binding Free Energy Calculations. Journal of Chemical Theory and Computation. PMID 31593627 DOI: 10.1021/Acs.Jctc.9B00499  0.72
2019 Ustach VD, Lakkaraju SKK, Jo S, Yu W, Jiang W, MacKerell AD. Optimization and Evaluation of the Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. Journal of Chemical Information and Modeling. PMID 31034213 DOI: 10.1021/Acs.Jcim.9B00210  0.68
2019 Park SJ, Lee J, Qi Y, Kern NR, Lee HS, Jo S, Joung I, Joo K, Lee J, Im W. CHARMM-GUI Glycan Modeler for Modeling and Simulation of Carbohydrates and Glycoconjugates. Glycobiology. PMID 30689864 DOI: 10.1093/Glycob/Cwz003  1
2019 Ustach VD, Lakkaraju SK, Jo S, Yu W, Lin F, Jiang W, MacKerell AD. Optimization of the Site-Identification by Ligand Competitive Saturation (SILCS) as an Accurate and Reliable Technique in Lead Optimization Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.2581  0.68
2018 Lee J, Patel DS, Ståhle J, Park SJ, Kern NR, Kim SH, Lee J, Cheng X, Valvano MA, Holst O, Knirel YA, Qi Y, Jo S, Klauda JB, Widmalm G, et al. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. Journal of Chemical Theory and Computation. PMID 30525595 DOI: 10.1021/Acs.Jctc.8B01066  1
2018 Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 30480445 DOI: 10.1021/Acs.Jctc.8B01075  0.72
2018 Jiang W, Thirman J, Jo S, Roux B. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. The Journal of Physical Chemistry. B. PMID 30253098 DOI: 10.1021/Acs.Jpcb.8B03277  0.72
2018 Sun D, Lakkaraju SK, Jo S, MacKerell AD. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water. Journal of Chemical Theory and Computation. PMID 30183291 DOI: 10.1021/Acs.Jctc.8B00604  0.44
2017 Jo S, Myatt D, Qi Y, Doutch J, Clifton LA, Im W, Widmalm G. Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study. The Journal of Physical Chemistry. B. PMID 29268602 DOI: 10.1021/Acs.Jpcb.7B11085  1
2017 Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 29111720 DOI: 10.1021/Acs.Jctc.7B00875  0.72
2017 Park SJ, Lee J, Patel DS, Ma H, Lee HS, Jo S, Im W. Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank. Bioinformatics (Oxford, England). PMID 28582506 DOI: 10.1093/Bioinformatics/Btx358  1
2017 Kim S, Lee J, Jo S, Brooks CL, Lee HS, Im W. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. Journal of Computational Chemistry. PMID 28497616 DOI: 10.1002/Jcc.24829  1
2016 Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry. PMID 27862047 DOI: 10.1002/Jcc.24660  1
2016 Jo S, Suh D, He Z, Chipot C, Roux B. Leveraging the Information from Markov State Models to Improve the Convergence of Umbrella Sampling Simulations. The Journal of Physical Chemistry. B. PMID 27409349 DOI: 10.1021/Acs.Jpcb.6B05125  1
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935  1
2015 Jo S, Chipot C, Roux B. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. Journal of Chemical Theory and Computation. 11: 2234-44. PMID 26574422 DOI: 10.1021/Ct501034W  0.72
2015 Qi Y, Jo S, Im W. Roles of Glycans in Interactions between gp120 and HIV Broadly Neutralizing Antibodies. Glycobiology. PMID 26537503 DOI: 10.1093/Glycob/Cwv101  1
2015 Jo S, Qi Y, Im W. Preferred Conformations of N-glycan Core Pentasaccharide in Solution and in Glycoproteins. Glycobiology. PMID 26405106 DOI: 10.1093/Glycob/Cwv083  1
2015 Du X, Zhang Y, Jo SR, Liu X, Qi Y, Osborne B, Byrne FL, Smith GC, Turner N, Hoehn KL, Brown AJ, Yang H. Akt Activation Increases Cellular Cholesterol by Promoting the Proteasomal Degradation of Niemann-Pick C1. The Biochemical Journal. PMID 26283546 DOI: 10.1042/BJ20150602  0.72
2015 Park MH, Yim HW, Park S, Lee C, Lee CU, Hong SC, Jeong JH, Seo HJ, Jeong SH, Jo SJ, Choi J. School refusal behavior in South Korean first graders: A prospective observational community-based study. Psychiatry Research. 227: 160-5. PMID 25908264 DOI: 10.1016/j.psychres.2015.04.011  0.44
2015 Cheng X, Jo S, Qi Y, Marassi FM, Im W. Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Biophysical Journal. 108: 1954-62. PMID 25902435 DOI: 10.1016/J.Bpj.2015.03.012  1
2015 Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W. GS-align for glycan structure alignment and similarity measurement. Bioinformatics (Oxford, England). PMID 25857669 DOI: 10.1093/Bioinformatics/Btv202  1
2015 Son Y, Yang M, Kang S, Lee S, Kim J, Kim J, Park S, Kim JS, Jo SK, Jung U, Shin T, Kim SH, Wang H, Moon C. Cranial irradiation regulates CREB-BDNF signaling and variant BDNF transcript levels in the mouse hippocampus. Neurobiology of Learning and Memory. 121: 12-9. PMID 25792232 DOI: 10.1016/J.Nlm.2015.03.002  0.44
2015 Mallajosyula SS, Jo S, Im W, MacKerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods in Molecular Biology (Clifton, N.J.). 1273: 407-29. PMID 25753723 DOI: 10.1007/978-1-4939-2343-4_25  0.36
2015 Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods in Molecular Biology (Clifton, N.J.). 1273: 391-406. PMID 25753722 DOI: 10.1007/978-1-4939-2343-4_24  0.36
2015 Jo S, Chipot C, Roux B. Efficient determination of relative entropy using combined temperature and hamiltonian replica-exchange molecular dynamics Journal of Chemical Theory and Computation. 11: 2234-2244. DOI: 10.1021/ct501034w  1
2015 Jo S, Jiang W. A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations Computer Physics Communications. 197: 304-311. DOI: 10.1016/J.Cpc.2015.08.030  0.68
2014 Lee HS, Shin KO, Jo SC, Lee YM, Yim YH. Optimized precursor ion selection for labile ions in a linear ion trap mass spectrometer and its impact on quantification using selected reaction monitoring. Journal of Mass Spectrometry : Jms. 49: 1234-8. PMID 25476940 DOI: 10.1002/jms.3450  0.68
2014 Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD, Roux B, Im W. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Advances in Protein Chemistry and Structural Biology. 96: 235-65. PMID 25443960 DOI: 10.1016/Bs.Apcsb.2014.06.002  1
2014 Kern NR, Lee HS, Wu EL, Park S, Vanommeslaeghe K, MacKerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophysical Journal. 107: 1885-95. PMID 25418169 DOI: 10.1016/J.Bpj.2014.09.007  1
2014 Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of Computational Chemistry. 35: 1997-2004. PMID 25130509 DOI: 10.1002/Jcc.23702  1
2014 Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. Plos Computational Biology. 10: e1003521. PMID 24699246 DOI: 10.1371/Journal.Pcbi.1003521  1
2014 Jeong JC, Jo S, Wu EL, Qi Y, Monje-Galvan V, Yeom MS, Gorenstein L, Chen F, Klauda JB, Im W. ST-analyzer: a web-based user interface for simulation trajectory analysis. Journal of Computational Chemistry. 35: 957-63. PMID 24638223 DOI: 10.1002/Jcc.23584  1
2014 Qi Y, Cheng X, Han W, Jo S, Schulten K, Im W. CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations. Journal of Chemical Information and Modeling. 54: 1003-9. PMID 24624945 DOI: 10.1021/Ci500007N  1
2013 Wu EL, Engström O, Jo S, Stuhlsatz D, Yeom MS, Klauda JB, Widmalm G, Im W. Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophysical Journal. 105: 1444-55. PMID 24047996 DOI: 10.1016/J.Bpj.2013.08.002  1
2013 Cheng X, Jo S, Marassi FM, Im W. NMR-based simulation studies of Pf1 coat protein in explicit membranes. Biophysical Journal. 105: 691-8. PMID 23931317 DOI: 10.1016/J.Bpj.2013.06.040  1
2013 Cheng X, Jo S, Lee HS, Klauda JB, Im W. CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. Journal of Chemical Information and Modeling. 53: 2171-80. PMID 23865552 DOI: 10.1021/Ci4002684  1
2013 Jo S, Lee HS, Skolnick J, Im W. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. Plos Computational Biology. 9: e1002946. PMID 23516343 DOI: 10.1371/Journal.Pcbi.1002946  1
2013 Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. Journal of Chemical Information and Modeling. 53: 267-77. PMID 23205773 DOI: 10.1021/Ci300505N  1
2013 Jo S, Im W. Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Research. 41: D470-4. PMID 23104379 DOI: 10.1093/Nar/Gks987  1
2012 Lee HS, Jo S, Lim HS, Im W. Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors. Journal of Chemical Information and Modeling. 52: 1821-32. PMID 22731511 DOI: 10.1021/Ci3000997  1
2012 Zhong D, Lefebre M, Kaur K, McDowell MA, Gdowski C, Jo S, Wang Y, Benedict SH, Lea SM, Galan JE, De Guzman RN. The Salmonella type III secretion system inner rod protein PrgJ is partially folded. The Journal of Biological Chemistry. 287: 25303-11. PMID 22654099 DOI: 10.1074/Jbc.M112.381574  1
2012 Kwon T, Roux B, Jo S, Klauda JB, Harris AL, Bargiello TA. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophysical Journal. 102: 1341-51. PMID 22455917 DOI: 10.1016/J.Bpj.2012.02.009  1
2012 Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W. Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. Journal of Computational Chemistry. 33: 331-9. PMID 22102176 DOI: 10.1002/Jcc.21952  1
2012 Im W, Jo S, Kim T. An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins. Biochimica Et Biophysica Acta. 1818: 252-62. PMID 21851810 DOI: 10.1016/J.Bbamem.2011.07.048  1
2011 Jo S, Song KC, Desaire H, MacKerell AD, Im W. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. Journal of Computational Chemistry. 32: 3135-41. PMID 21815173 DOI: 10.1002/Jcc.21886  1
2011 Kim T, Jo S, Im W. Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophysical Journal. 100: 2922-8. PMID 21689525 DOI: 10.1016/J.Bpj.2011.02.063  1
2011 Jo S, Im W. Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. Biophysical Journal. 100: 2913-21. PMID 21689524 DOI: 10.1016/J.Bpj.2011.05.009  1
2011 Lee JH, Zhang Q, Jo S, Chai SC, Oh M, Im W, Lu H, Lim HS. Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions. Journal of the American Chemical Society. 133: 676-9. PMID 21171592 DOI: 10.1021/Ja108230S  1
2010 Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. The Journal of Physical Chemistry. B. 114: 13342-8. PMID 20923227 DOI: 10.1021/Jp108166K  1
2009 Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophysical Journal. 97: 50-8. PMID 19580743 DOI: 10.1016/J.Bpj.2009.04.013  1
2008 Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Research. 36: W270-5. PMID 18508808 DOI: 10.1093/Nar/Gkn314  1
2008 Jo S, Kim T, Iyer VG, Im W. CHARMM-GUI: a web-based graphical user interface for CHARMM. Journal of Computational Chemistry. 29: 1859-65. PMID 18351591 DOI: 10.1002/Jcc.20945  1
2007 Jo S, Kim T, Im W. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. Plos One. 2: e880. PMID 17849009 DOI: 10.1371/Journal.Pone.0000880  1
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