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Sunhwan Jo

TitlePost Doctoral Scholar
InstitutionUniversity of Chicago
DepartmentBiochem/Mol Bio
AddressChicago IL 60637
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    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Kognole AA, Lee J, Park SJ, Jo S, Chatterjee P, Lemkul JA, Huang J, MacKerell AD, Im W. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. J Comput Chem. 2022 02 15; 43(5):359-375. PMID: 34874077.
      View in: PubMed
    2. Choi YK, Kern NR, Kim S, Kanhaiya K, Afshar Y, Jeon SH, Jo S, Brooks BR, Lee J, Tadmor EB, Heinz H, Im W. CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems. J Chem Theory Comput. 2022 Jan 11; 18(1):479-493. PMID: 34871001.
      View in: PubMed
    3. Goel H, Hazel A, Yu W, Jo S, MacKerell AD. Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design. New J Chem. 2022 Jan 21; 46(3):919-932. PMID: 35210743.
      View in: PubMed
    4. Goel H, Hazel A, Ustach VD, Jo S, Yu W, MacKerell AD. Rapid and accurate estimation of protein-ligand relative binding affinities using site-identification by ligand competitive saturation. Chem Sci. 2021 Jul 01; 12(25):8844-8858. PMID: 34257885.
      View in: PubMed
    5. Takimoto T, Sasaki H, Tsue H, Takahashi H, MacKerell AD, Nakamura A, Nakano K, Okazaki E, 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. 2021 Jan 21; 27(5):1648-1654. PMID: 33258147.
      View in: PubMed
    6. 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). J Pharm Sci. 2021 03; 110(3):1103-1110. PMID: 33137372.
      View in: PubMed
    7. 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-Biologics Approach. Mol Pharm. 2020 11 02; 17(11):4323-4333. PMID: 32965126.
      View in: PubMed
    8. 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). Biochim Biophys Acta Gen Subj. 2020 04; 1864(4):129519. PMID: 31911242.
      View in: PubMed
    9. Suh D, Jo S, Jiang W, Chipot C, Roux B. String Method for Protein-Protein Binding Free-Energy Calculations. J Chem Theory Comput. 2019 Nov 12; 15(11):5829-5844. PMID: 31593627.
      View in: PubMed
    10. Ustach VD, Lakkaraju SK, Jo S, Yu W, Jiang W, MacKerell AD. Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. J Chem Inf Model. 2019 06 24; 59(6):3018-3035. PMID: 31034213.
      View in: PubMed
    11. 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. 2019 04 01; 29(4):320-331. PMID: 30689864.
      View in: PubMed
    12. Yu W, Jo S, Lakkaraju SK, Weber DJ, MacKerell AD. Exploring protein-protein interactions using the site-identification by ligand competitive saturation methodology. Proteins. 2019 04; 87(4):289-301. PMID: 30582220.
      View in: PubMed
    13. Lee J, Patel DS, Ståhle J, Park SJ, Kern NR, Kim S, Lee J, Cheng X, Valvano MA, Holst O, Knirel YA, Qi Y, Jo S, Klauda JB, Widmalm G, Im W. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. J Chem Theory Comput. 2019 Jan 08; 15(1):775-786. PMID: 30525595.
      View in: PubMed
    14. 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. J Chem Theory Comput. 2018 12 11; 14(12):6748-6749. PMID: 30480445.
      View in: PubMed
    15. Jiang W, Thirman J, Jo S, Roux B. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. J Phys Chem B. 2018 10 18; 122(41):9435-9442. PMID: 30253098.
      View in: PubMed
    16. 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. J Chem Theory Comput. 2018 Oct 09; 14(10):5290-5302. PMID: 30183291.
      View in: PubMed
    17. 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. J Phys Chem B. 2018 01 25; 122(3):1169-1175. PMID: 29268602.
      View in: PubMed
    18. 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. J Chem Theory Comput. 2017 Dec 12; 13(12):5933-5944. PMID: 29111720.
      View in: PubMed
    19. 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. 2017 Oct 01; 33(19):3051-3057. PMID: 28582506.
      View in: PubMed
    20. 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. J Comput Chem. 2017 06 05; 38(21):1879-1886. PMID: 28497616.
      View in: PubMed
    21. 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, Im W. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem. 2017 06 05; 38(15):1114-1124. PMID: 27862047.
      View in: PubMed
    22. 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. J Phys Chem B. 2016 08 25; 120(33):8733-42. PMID: 27409349.
      View in: PubMed
    23. 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, Klauda JB, Im W. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J Chem Theory Comput. 2016 Jan 12; 12(1):405-13. PMID: 26631602.
      View in: PubMed
    24. Qi Y, Jo S, Im W. Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies. Glycobiology. 2016 Mar; 26(3):251-60. PMID: 26537503.
      View in: PubMed
    25. Jo S, Qi Y, Im W. Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. Glycobiology. 2016 Jan; 26(1):19-29. PMID: 26405106.
      View in: PubMed
    26. Jo S, Chipot C, Roux B. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. J Chem Theory Comput. 2015 May 12; 11(5):2234-44. PMID: 26574422.
      View in: PubMed
    27. Cheng X, Jo S, Qi Y, Marassi FM, Im W. Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Biophys J. 2015 Apr 21; 108(8):1954-62. PMID: 25902435.
      View in: PubMed
    28. Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W. GS-align for glycan structure alignment and similarity measurement. Bioinformatics. 2015 Aug 15; 31(16):2653-9. PMID: 25857669.
      View in: PubMed
    29. Mallajosyula SS, Jo S, Im W, MacKerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol. 2015; 1273:407-29. PMID: 25753723.
      View in: PubMed
    30. Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods Mol Biol. 2015; 1273:391-406. PMID: 25753722.
      View in: PubMed
    31. 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. Biophys J. 2014 Oct 21; 107(8):1885-1895. PMID: 25418169.
      View in: PubMed
    32. 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. Adv Protein Chem Struct Biol. 2014; 96:235-65. PMID: 25443960.
      View in: PubMed
    33. 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. J Comput Chem. 2014 Oct 15; 35(27):1997-2004. PMID: 25130509.
      View in: PubMed
    34. 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 Comput Biol. 2014 Apr; 10(4):e1003521. PMID: 24699246.
      View in: PubMed
    35. 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. J Comput Chem. 2014 May 05; 35(12):957-63. PMID: 24638223.
      View in: PubMed
    36. 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. J Chem Inf Model. 2014 Mar 24; 54(3):1003-9. PMID: 24624945.
      View in: PubMed
    37. 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. Biophys J. 2013 Sep 17; 105(6):1444-55. PMID: 24047996.
      View in: PubMed
    38. Cheng X, Jo S, Marassi FM, Im W. NMR-based simulation studies of Pf1 coat protein in explicit membranes. Biophys J. 2013 Aug 06; 105(3):691-8. PMID: 23931317.
      View in: PubMed
    39. Cheng X, Jo S, Lee HS, Klauda JB, Im W. CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. J Chem Inf Model. 2013 Aug 26; 53(8):2171-80. PMID: 23865552.
      View in: PubMed
    40. Jo S, Lee HS, Skolnick J, Im W. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol. 2013; 9(3):e1002946. PMID: 23516343.
      View in: PubMed
    41. Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. J Chem Inf Model. 2013 Jan 28; 53(1):267-77. PMID: 23205773.
      View in: PubMed
    42. Jo S, Im W. Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res. 2013 Jan; 41(Database issue):D470-4. PMID: 23104379.
      View in: PubMed
    43. 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. J Chem Inf Model. 2012 Jul 23; 52(7):1821-32. PMID: 22731511.
      View in: PubMed
    44. 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. Biophys J. 2012 Mar 21; 102(6):1341-51. PMID: 22455917.
      View in: PubMed
    45. 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. J Comput Chem. 2012 Jan 30; 33(3):331-9. PMID: 22102176.
      View in: PubMed
    46. Im W, Jo S, Kim T. An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins. Biochim Biophys Acta. 2012 Feb; 1818(2):252-62. PMID: 21851810.
      View in: PubMed
    47. Jo S, Song KC, Desaire H, MacKerell AD, Im W. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J Comput Chem. 2011 Nov 15; 32(14):3135-41. PMID: 21815173.
      View in: PubMed
    48. Jo S, Im W. Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. Biophys J. 2011 Jun 22; 100(12):2913-21. PMID: 21689524.
      View in: PubMed
    49. Kim T, Jo S, Im W. Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophys J. 2011 Jun 22; 100(12):2922-8. PMID: 21689525.
      View in: PubMed
    50. Lee JH, Zhang Q, Jo S, Chai SC, Oh M, Im W, Lu H, Lim HS. Novel pyrrolopyrimidine-based a-helix mimetics: cell-permeable inhibitors of protein-protein interactions. J Am Chem Soc. 2011 Feb 02; 133(4):676-9. PMID: 21171592.
      View in: PubMed
    51. Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. J Phys Chem B. 2010 Oct 28; 114(42):13342-8. PMID: 20923227.
      View in: PubMed
    52. Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J. 2009 Jul 08; 97(1):50-8. PMID: 19580743.
      View in: PubMed
    53. Jo SH, Hong HK, Chong SH, Lee HS, Choe H. H(1) antihistamine drug promethazine directly blocks hERG K(+) channel. Pharmacol Res. 2009 Nov; 60(5):429-37. PMID: 19497368.
      View in: PubMed
    54. Kim YJ, Hong HK, Lee HS, Moh SH, Park JC, Jo SH, Choe H. Papaverine, a vasodilator, blocks the pore of the HERG channel at submicromolar concentration. J Cardiovasc Pharmacol. 2008 Dec; 52(6):485-93. PMID: 19034039.
      View in: PubMed
    55. Jo S, Kim T, Iyer VG, Im W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem. 2008 Aug; 29(11):1859-65. PMID: 18351591.
      View in: PubMed
    56. Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W270-5. PMID: 18508808.
      View in: PubMed
    57. Jo S, Kim T, Im W. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. PLoS One. 2007 Sep 12; 2(9):e880. PMID: 17849009.
      View in: PubMed
    58. Choe H, Nah KH, Lee SN, Lee HS, Lee HS, Jo SH, Leem CH, Jang YJ. A novel hypothesis for the binding mode of HERG channel blockers. Biochem Biophys Res Commun. 2006 May 26; 344(1):72-8. PMID: 16616004.
      View in: PubMed
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