sunhwanj.com

This is my personal blog.

Publications

This is a list of my academic publications. See my Google Scholar Profile also.

Articles

  1. Exploring protein‐protein interactions using the site‐identification by ligand competitive saturation methodology
    Wenbo Yu, Sunhwan Jo, Sirish Kaushik Lakkaraju, David J Weber, Alexander D MacKerell Jr.
    Proteins (2018)
    [DOI]
  2. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans
    Jumin Lee, Dhilon S Patel, Jonas Ståhle, Sang-Jun Park, Nathan R Kern, Seonghoon Kim, Joonseong Lee, Xi Cheng, Miguel A Valvano, Otto Holst, Yuriy A Knirel, Yifei Qi, Sunhwan Jo, Jeffery B Klauda, Göran Widmalm, Wonpil Im.
    J. Chem. Theory Compute. (2019) 15:775–786
    [DOI]
  3. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis
    Wei Jiang, Jonathan Thirman, Sunhwan Jo, Benoît Roux.
    J. Phys. Chem. B (2018) 122:9435–9442
    [DOI]
  4. Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study
    Sunhwan Jo, Daniel Myatt, Yifei Qi, James Doutch, Luke A Clifton, Wonpil Im, Göran Widmalm.
    J. Phys. Chem. B (2018) 122:1169-1175
    [DOI]
  5. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
    Brian K Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C Phillips, Klaus Schulten, Benoît Roux.
    J. Chem. Theory Compute. (2017) 13:5933-5944
    [DOI]
  6. Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank
    Sang-Jun Park, Jumin Lee, Dhilon S Patel, Hongjing Ma, Hui Sun Lee, Sunhwan Jo, Wonpil Im.
    Bioinformatics (2017) 33:3051–3057
    [DOI]
  7. CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules
    Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L Brooks III, Hui Sun Lee, Wonpil Im.
    J. Comput. Chem. (2017) 38:1879-1886
    [DOI]
  8. CHARMM‐GUI 10 years for biomolecular modeling and simulation
    Sunhwan Jo, Xi Cheng, Jumin Lee, Seonghoon Kim, Sang‐Jun Park, Dhilon S Patel, Andrew H Beaven, Kyu Il Lee, Huan Rui, Soohyung Park, Hui Sun Lee, Benoît Roux, Alexander D MacKerell Jr, Jeffrey B Klauda, Yifei Qi, Wonpil Im.
    J. Comput. Chem. (2017) 38:1114-1124
    [DOI]
  9. Leveraging the Information from Markov State Models to Improve the Convergence of Umbrella Sampling Simulations
    Sunhwan Jo, Donghyuk Suh, Ziwei He, Christophe Chipot, Benoît Roux.
    J. Phys. Chem. B (2016) 120:8733-8742
    [DOI]
  10. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field
    Jumin Lee, Xi Cheng, Jason M Swails, Min Sun Yeom, Peter Kenneth Eastman, Justin A Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S Pande, David A Case, Charles L Brooks, Alexander D MacKerell, Jeffery B Klauda, Wonpil Im.
    J. Chem. Theory Compute. (2015)
    [charmm-gui.org | DOI]
  11. Roles of Glycans in Interactions between gp120 and HIV Broadly Neutralizing Antibodies
    Yifei Qi, Sunhwan Jo, Wonpil Im.
    Glycobiology (2015)
    [DOI]
  12. Preferred Conformations of N-glycan Core Pentasaccharide in Solution and in Glycoproteins
    Sunhwan Jo, Yifei Qi, Wonpil Im.
    Glycobiology (2016) 26:19-29
    [DOI]
  13. A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations
    Sunhwan Jo, Wei Jiang.
    Compute. Phys. Comm. (2015) 197:304-311
    [DOI | GitHub]
  14. Efficient determination of relative entropy using combined temperature and Hamiltonian replica-exchange molecular dynamics
    Sunhwan Jo, Chris Chipot, Benoît Roux.
    J. Chem. Theory Comput. (2015) 11:2234-2244
    [DOI | GitHub]
  15. GS-align for Glycan Structure Alignment and Similarity Measurement
    Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee, Wonpil Im.
    Bioinformatics (2015)
    [DOI]
  16. Solid-State NMR Observable-based Ensemble Dynamics Simulations of Membrane Protein in Explicit Membranes
    Xi Cheng, Sunhwan Jo, Yifei Qi, Francesca M Marassi, and Wonpil Im.
    Biophys. J. (2015) 108:1954-1962
    [DOI]
  17. Lipid-Linked Oligosaccharides in Membranes Sample Conformations That Facilitate Binding to Oligosaccharyltransferase
    Nathan R Kern, Hui Sun Lee, Emilia L Wu, Soohyung Park, Kenno Vanommeslaeghe, Alexander D MacKerell, Jeffery B Klauda, Sunhwan Jo, Wonpil Im.
    Biophys. J. (2014) 107(8):1885-1895
    [DOI]
  18. CHARMM-GUI <i>Membrane Builder</i> toward realistic biological membrane simulations
    Emilia L Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C Song, Eder M Davilia-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M Venable, Jeffery B Klauda, Wonpil Im.
    J. Comput. Chem. (2014) 35(27):1997-2004
    [charmm-gui.org/input/membrane | DOI]
  19. Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
    Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, and Benoît Roux.
    PLoS Comput. Biol. (2014) 10(4):e1003521
    [anmpathway.lcrc.anl.gov | DOI | GitHub]
  20. ST‐analyzer: A web‐based user interface for simulation trajectory analysis
    Jong Cheol Jeong, Sunhwan Jo, Emilia L Wu, Yifei Qi, Viviana Monje‐Galvan, Min Sun Yeom, Lev Gorenstein, Feng Chen, Jeffery B Klauda, Wonpil Im.
    J. Comput. Chem. (2014) 35(12):957-963
    [im.bioinformatics.ku.edu/st-analyzer | DOI]
  21. CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations
    Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, and Wonpil Im.
    J. Chem. Inf. Model. (2014) 54(3):1003-1009
    [www.charmm-gui.org/input/cgbilayer | DOI]
  22. Molecular Dynamics and NMR Spectroscopy Studies of <i>E. coli</i> Lipopolysaccharide Structure and Dynamics
    Emilia L Wu, Olof Engström, Sunhwan Jo, Danielle Stuhlsatz, Min Sun Yeom, Jeffery B Klauda, Göran Widmalm, and Wonpil Im.
    Biophys. J. (2013) 105(6):1444-1455
    [DOI]
  23. CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems
    Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffrey Klauda, and Wonpil Im.
    J. Chem. Inf. Model. (2013) 53(8):2171-2180
    [www.charmm-gui.org/input/micelle | DOI | PDF]
  24. NMR-Based simulation studies of pf1 coat protein in explicit membranes
    Xi Cheng, Sunhwan Jo, Francesca M Marassi, Wonpil Im.
    Biophys. J. (2013) 105(3):691-698
    [DOI]
  25. Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling
    Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, and Wonpil Im.
    PLoS Comput. Biol. (2013) 9(3):e1002946
    [DOI]
  26. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
    Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, and Wonpil Im.
    J. Chem. Inf. Model. (2013) 53(1):267-277
    [www.charmm-gui.org/input/gbind | DOI]
  27. Glycan Fragment DB: A Database of PDB-Based Glycan 3D Structures
    Sunhwan Jo and Wonpil Im.
    Nucleic Acid Res. (2013) 41(D1):D470-D474
    [glycanstructure.org/fragment | DOI]
  28. Application of Absolute Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors
    Hui Sun Lee, Sunhwan Jo, Hyun-Suk Lim, and Wonpil Im.
    J. Chem. Inf. Model. (2012) 52(7):1821-1832
    [DOI]
  29. The Salmonella Type III Secretion System Inner Rod Protein PrgJ Is Partially Folded
    Dalian Zhong, Matthew Lefebre, Kawaljit Kaur, Melanie A McDowell, Courtney Godwski, Sunhwan Jo, Yu Wang, Stephen H Benedict, Susan M Lea, Jorge E Galan, and Roberto De. Guzman.
    J. Biol. Chem (2012) 287(30):25303-25311
    [DOI]
  30. Molecular Dynamics Simulation of the Cx26 Hemichannel: Insight Into Voltage-Dependent Loop-Gating
    Taekyung Kwon, Benoît Roux, Sunhwan Jo, Jeffery B. Klauda, Andrew L. Harris, and Thaddeus A. Bargiello.
    Biophys. J. (2012) 102(6):1341-1351 (Selected as cover)
    [DOI]
  31. Web Interface for Brownian Dynamics Simulation of Ion Transport and Its Applications to Beta-Barrel Pores
    Kyuil Lee, Sunhwan Jo, Huan Rui, Bernhard Egwolf, Benoît Roux, Richard Paster, and Wonpil Im.
    J. Comput. Chem. (2012) 33(3):331-339 (Selected as cover)
    [charmm-gui.org/input/gcmcbd | DOI]
  32. An Ensemble Dynamics Approach to Decipher Solid-state NMR Observables of Membrane Proteins
    Wonpil Im, Sunhwan Jo, and Taehoon Kim.
    Biochim. Biophys. Acta (2012) 1818(2):252-262
    [DOI]
  33. Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins
    Sunhwan Jo, Kevin Song, Heather Desaire, Alexander D. MacKerell, Jr., and Wonpil Im.
    J. Comput. Chem. (2011) 32(14):3135-3141 (Selected as cover)
    [charmm-gui.org/input/glycan | DOI]
  34. Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables
    Sunhwan Jo and Wonpil Im.
    Biophys. J. (2011) 100(12):2913-2921
    [DOI]
  35. Solid-State NMR Ensemble Dynamics as a Mediator between Experiment and Simulation
    Taehoon Kim, Sunhwan Jo, Wonpil Im.
    Biophys. J. (2011) 100(12):2922-2928
    [DOI]
  36. Novel Pyrrolopyrimidine-Based α-Helix Mimetics: Cell-Permeable Inhibitors of Protein-Protein Interactions
    Ji Hoon Lee, Qi Zhang, Sunhwan Jo, Sergio Cha, Misook Oh, Wonpil Im, Hua Lu, Hyun-Suk Lim.
    J Am. Chem. Soc. (2011) 33(4):676-679
    [DOI]
  37. Cholesterol flip-flop: insights from free energy simulation studies
    Sunhwan Jo, Huan Rui, Joseph. B. Lim, Jeffrey B. Klauda, Wonpil Im.
    J. Phys. Chem. B. (2010) 114(42):13342-13348
    [DOI]
  38. CHARMM-GUI Membrane Builder for Mixed Bilayers and Its application to Yeast Membrane
    Sunhwan Jo, Joseph B. Lim, Jeffery B. Klauda, and Wonpil Im.
    Biophys. J. (2009) 97(1):50-58
    [charmm-gui.org/input/membrane | DOI]
  39. PBEQ-Solver for Online Visualization of Electrostatic Potential of Biomolecules
    Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, and Wonpil Im.
    Nucleic Acids Res (2008) 36(Web Server Issue):W270-W275
    [charmm-gui.org/input/pbeqsolver | DOI]
  40. CHARMM-GUI: Web-based Graphical User Interface for CHARMM
    Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, and Wonpil Im.
    J. Comput. Chem. (2008) 29(11):1859-1865
    [charmm-gui.org | DOI]
  41. Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
    Sunhwan Jo, Taehoon Kim, and Wonpil Im.
    PLoS ONE (2007) 2(9):e880
    [charmm-gui.org/input/membrane | DOI | PDF]

Book chapters

  1. Lipopolysaccharide Membrane Building and Simulation.
    Sunhwan Jo, Emilia Wu, Danielle Stuhlsatz, Jeffery B. Klauda, Göran Wildmalm, and Wonpil Im.
    Methods in Molecular Biology: Glycoinformatics (2015)
    [DOI]
  2. Molecular Dynamics Simulations of Glycoproteins using CHARMM.
    Sairam S. Mallajosyula, Sunhwan Jo, Wonpil Im, and Alexander D. MacKerell, Jr..
    Methods in Molecular Biology: Glycoinformatics (2015)
    [DOI | PDF]
  3. CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues.
    Sunhwan Jo, Xi Cheng, Shahidul M. Islam, Lei Huang, Huan Rui, Allen Zhu, Hui Sun Lee, Yifei Qi, Wei Han, Kenno Vanommeslaeghe, Alexander D. MacKerell Jr., Benoît Roux, Wonpil Im.
    Advances in Protein Chemistry and Structural Biology (2015)
    [DOI]
  4. Computational Studies of Glycan Conformations in Glycoproteins
    Sunhwan Jo.
    Ph.D. Thesis (2015)
    [DOI]