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Sunhwan Jo

TitlePost Doctoral Scholar
InstitutionUniversity of Chicago
DepartmentBiochemistry and Molecular Biology
AddressChicago IL 60637
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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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Chung J, Bhatt A, Levine JE, Lin YC, Zhao M, MacKerell AD, Jo S, Kosaraju SC, Luo YL. Docking-score landscapes shape active-learning performance across Vina, Glide, and SILCS. J Comput Aided Mol Des. 2026 Sep 11; 40(1). PMID: 42726342; PMCID: PMC13569507.
      Citations:    
    2. Jiang W, Wijerathne TD, Zhang H, Lin YC, Jo S, Im W, Lacroix JJ, Luo YL. Structural and thermodynamic framework for PIEZO1 modulation by small molecules. Proc Natl Acad Sci U S A. 2023 12 12; 120(50):e2310933120. PMID: 38060566; PMCID: PMC10723123.
      Citations: 14     Fields:    Translation:Cells
    3. Zhao M, Kognole AA, Jo S, Tao A, Hazel A, MacKerell AD. GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. J Comput Chem. 2023 Jul 30; 44(20):1719-1732. PMID: 37093676; PMCID: PMC10330275.
      Citations: 6     Fields:    
    4. 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; PMCID: PMC8741736.
      Citations: 24     Fields:    Translation:Cells
    5. 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; PMCID: PMC8752518.
      Citations: 57     Fields:    
    6. 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; PMCID: PMC8863107.
      Citations: 14     
    7. 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; PMCID: PMC8246086.
      Citations: 28     
    8. 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; PMCID: PMC7887132.
      Citations:    Fields:    
    9. 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; PMCID: PMC7897284.
      Citations: 13     Fields:    
    10. 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; PMCID: PMC7606568.
      Citations: 23     Fields:    Translation:Cells
    11. 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; PMCID: PMC7029399.
      Citations: 38     Fields:    Translation:HumansCells
    12. 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.
      Citations: 14     Fields:    Translation:Cells
    13. 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; PMCID: PMC6597307.
      Citations: 51     Fields:    Translation:Cells
    14. 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; PMCID: PMC6422236.
      Citations: 179     Fields:    Translation:Cells
    15. 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; PMCID: PMC6408985.
      Citations: 21     Fields:    Translation:HumansAnimalsCells
    16. Lee J, Patel DS, Park SJ, Kern NR, Kim S, Lee J, Cheng X, Valvano MA, Holst O, Knirel YA, Qi Y, Jo S, Klauda JB, Im W, Ståhle J, Widmalm G. 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.
      Citations: 325     Fields:    Translation:HumansCells
    17. 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; PMCID: PMC11674073.
      Citations: 1     Fields:    
    18. 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; PMCID: PMC6339808.
      Citations: 21     Fields:    Translation:Cells
    19. 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; PMCID: PMC6195813.
      Citations: 11     Fields:    
    20. 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.
      Citations: 3     Fields:    Translation:Cells
    21. Radak BK, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Chipot C, Roux B. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theory Comput. 2017 Dec 12; 13(12):5933-5944. PMID: 29111720; PMCID: PMC5726918.
      Citations: 87     Fields:    Translation:Cells
    22. 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; PMCID: PMC5870669.
      Citations: 72     Fields:    
    23. 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; PMCID: PMC5488718.
      Citations: 282     Fields:    
    24. Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, MacKerell AD, Klauda JB, Qi Y, Im W, Roux B. CHARMM-GUI 10 years for biomolecular modeling and simulation. J Comput Chem. 2017 06 05; 38(15):1114-1124. PMID: 27862047; PMCID: PMC5403596.
      Citations: 162     Fields:    Translation:HumansAnimalsCells
    25. 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.
      Citations: 6     Fields:    
    26. 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; PMCID: PMC4712441.
      Citations: 1951     Fields:    Translation:Cells
    27. 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; PMCID: PMC4736541.
      Citations: 10     Fields:    Translation:HumansCells
    28. 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; PMCID: PMC4672150.
      Citations: 17     Fields:    Translation:Cells
    29. 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.
      Citations: 3     Fields:    Translation:Cells
    30. 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; PMCID: PMC4407261.
      Citations: 6     Fields:    Translation:Cells
    31. 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; PMCID: PMC4528633.
      Citations: 6     Fields:    Translation:HumansCells
    32. Mallajosyula SS, Jo S, Im W, MacKerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods Mol Biol. 2015; 1273:407-29. PMID: 25753723; PMCID: PMC4537648.
      Citations: 16     Fields:    Translation:AnimalsCells
    33. Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Im W, Widmalm G. Lipopolysaccharide membrane building and simulation. Methods Mol Biol. 2015; 1273:391-406. PMID: 25753722; PMCID: PMC4484582.
      Citations: 22     Fields:    Translation:Cells
    34. 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; PMCID: PMC4213670.
      Citations: 16     Fields:    Translation:Cells
    35. Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD, Im W, Roux B. 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; PMCID: PMC4739825.
      Citations: 177     Fields:    Translation:HumansAnimalsCells
    36. Wu EL, Cheng X, Jo S, Rui H, Song KC, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W, Dávila-Contreras EM. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem. 2014 Oct 15; 35(27):1997-2004. PMID: 25130509; PMCID: PMC4165794.
      Citations: 1281     Fields:    Translation:Cells
    37. 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; PMCID: PMC3974643.
      Citations: 63     Fields:    Translation:Cells
    38. 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.
      Citations: 8     Fields:    Translation:Cells
    39. 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; PMCID: PMC3985889.
      Citations: 37     Fields:    
    40. Wu EL, Jo S, Stuhlsatz D, Yeom MS, Klauda JB, Im W, Engström O, Widmalm G. Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophys J. 2013 Sep 17; 105(6):1444-55. PMID: 24047996; PMCID: PMC3785875.
      Citations: 69     Fields:    Translation:Cells
    41. 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; PMCID: PMC3736739.
      Citations: 15     Fields:    Translation:Cells
    42. 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.
      Citations: 60     Fields:    Translation:Cells
    43. 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; PMCID: PMC3597548.
      Citations: 15     Fields:    Translation:Cells
    44. Jo S, Jiang W, Lee HS, Im W, Roux B. 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; PMCID: PMC3557591.
      Citations: 45     Fields:    Translation:Cells
    45. 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; PMCID: PMC3531216.
      Citations: 29     Fields:    Translation:Cells
    46. 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; PMCID: PMC3480999.
      Citations: 17     Fields:    Translation:HumansCells
    47. Kwon T, Jo S, Klauda JB, Harris AL, Bargiello TA, Roux B. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophys J. 2012 Mar 21; 102(6):1341-51. PMID: 22455917; PMCID: PMC3309406.
      Citations: 28     Fields:    Translation:Cells
    48. Lee KI, Jo S, Rui H, Egwolf B, Pastor RW, Im W, Roux B. 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; PMCID: PMC3240732.
      Citations: 23     Fields:    
    49. 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.
      Citations: 17     Fields:    Translation:HumansCells
    50. 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; PMCID: PMC3188666.
      Citations: 125     Fields:    Translation:Cells
    51. 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; PMCID: PMC3123920.
      Citations: 14     Fields:    Translation:Cells
    52. 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; PMCID: PMC3123927.
      Citations: 13     Fields:    Translation:Cells
    53. 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; PMCID: PMC3079198.
      Citations: 49     Fields:    Translation:HumansCells
    54. 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.
      Citations: 39     Fields:    Translation:Cells
    55. 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; PMCID: PMC2711372.
      Citations: 831     Fields:    Translation:AnimalsCells
    56. 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.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    57. 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.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    58. 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.
      Citations: 4081     Fields:    Translation:Cells
    59. Jo S, Vargyas M, Vasko-Szedlar J, Im W, Roux B. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res. 2008 Jul 01; 36(Web Server issue):W270-5. PMID: 18508808; PMCID: PMC2447802.
      Citations: 116     Fields:    Translation:Cells
    60. 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; PMCID: PMC1963319.
      Citations: 603     Fields:    Translation:Cells
    61. 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.
      Citations: 10     Fields:    Translation:HumansCells
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