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Publications
- 2022
[j47]Abhishek A. Kognole
, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell Jr., Wonpil Im:
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. J. Comput. Chem. 43(5): 359-375 (2022)- 2017
- [j31]Sang-Jun Park, Jumin Lee, Dhilon S. Patel, Hongjing Ma, Hui Sun Lee, Sunhwan Jo, Wonpil Im:
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank. Bioinform. 33(19): 3051-3057 (2017) - [j29]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:
CHARMM-GUI 10 years for biomolecular modeling and simulation. J. Comput. Chem. 38(15): 1114-1124 (2017) - [j28]Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L. Brooks III, Hui Sun Lee, Wonpil Im:
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. J. Comput. Chem. 38(21): 1879-1886 (2017) - 2015
- [j26]Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee, Wonpil Im:
GS-align for glycan structure alignment and similarity measurement. Bioinform. 31(16): 2653-2659 (2015) - 2014
- [j24]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:
ST-analyzer: A web-based user interface for simulation trajectory analysis. J. Comput. Chem. 35(12): 957-963 (2014) - [j23]Emilia L. Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C. Song, Eder M. Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M. Venable, Jeffery B. Klauda, Wonpil Im:
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J. Comput. Chem. 35(27): 1997-2004 (2014) - [j22]Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, Wonpil Im:
CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations. J. Chem. Inf. Model. 54(3): 1003-1009 (2014) - 2013
- [j21]Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, Wonpil Im:
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. J. Chem. Inf. Model. 53(1): 267-277 (2013) - [j20]Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffery B. Klauda, Wonpil Im:
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems. J. Chem. Inf. Model. 53(8): 2171-2180 (2013) - [j18]Sunhwan Jo, Wonpil Im:
Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res. 41(Database-Issue): 470-474 (2013) - [j17]Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im:
Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. PLoS Comput. Biol. 9(3) (2013) - 2012
- [j16]Kyu Il Lee, Sunhwan Jo, Huan Rui, Bernhard Egwolf, Benoît Roux, Richard W. Pastor, Wonpil Im:
Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores. J. Comput. Chem. 33(3): 331-339 (2012) - [j15]Hui Sun Lee, Sunhwan Jo, Hyun-Suk Lim, Wonpil Im:
Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors. J. Chem. Inf. Model. 52(7): 1821-1832 (2012) - 2011
- [j13]Sunhwan Jo, Kevin C. Song, Heather Desaire, Alexander D. MacKerell Jr., Wonpil Im:
Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J. Comput. Chem. 32(14): 3135-3141 (2011) - 2008
- [j7]Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im:
CHARMM-GUI: A web-based graphical user interface for CHARMM. J. Comput. Chem. 29(11): 1859-1865 (2008) - [j6]Sunhwan Jo, Miklós Vargyas, Judit Vasko-Szedlar, Benoît Roux, Wonpil Im:
PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Res. 36(Web-Server-Issue): 270-275 (2008)
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