CHARMM-GUI: A web-based graphical user interface for CHARMM. - Sunhwan Jo; Taehoon Kim; Vidyashankara G. Iyer; Wonpil Im (J. Comput. Chem., 2008)

PBEQ-Solver for online visualization of electrostatic potential of biomolecules. - Sunhwan Jo; Miklós Vargyas; Judit Vasko-Szedlar; Benoît Roux; Wonpil Im (Nucleic Acids Res., 2008)

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins. - Sunhwan Jo; Kevin C. Song; Heather Desaire; Alexander D. MacKerell Jr.; Wonpil Im (J. Comput. Chem., 2011)

Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores. - Kyu Il Lee; Sunhwan Jo; Huan Rui; Bernhard Egwolf; Benoît Roux; Richard W. Pastor; Wonpil Im (J. Comput. Chem., 2012)

Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors. - Hui Sun Lee; Sunhwan Jo; Hyun-Suk Lim; Wonpil Im (J. Chem. Inf. Model., 2012)

CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems. - Xi Cheng; Sunhwan Jo; Hui Sun Lee; Jeffery B. Klauda; Wonpil Im (J. Chem. Inf. Model., 2013)

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. - Sunhwan Jo; Wei Jiang; Hui Sun Lee; Benoît Roux; Wonpil Im (J. Chem. Inf. Model., 2013)

Glycan fragment database: a database of PDB-based glycan 3D structures. - Sunhwan Jo; Wonpil Im (Nucleic Acids Res., 2013)

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. - Sunhwan Jo; Hui Sun Lee; Jeffrey Skolnick; Wonpil Im (PLoS Comput. Biol., 2013)

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)

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. - 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 (J. Comput. Chem., 2014)

CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations. - Yifei Qi; Xi Cheng; Wei Han; Sunhwan Jo; Klaus Schulten; Wonpil Im (J. Chem. Inf. Model., 2014)

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; Benoît Roux (PLoS Comput. Biol., 2014)

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 (Bioinform., 2015)

A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations. - Sunhwan Jo; Wei Jiang (Comput. Phys. Commun., 2015)

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 (Bioinform., 2017)

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; et al. (J. Comput. Chem., 2017)

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)

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. - Vincent D. Ustach; Sirish Kaushik Lakkaraju; Sunhwan Jo; Wenbo Yu 002; Wenjuan Jiang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2019)

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. - Abhishek A. Kognole; Jumin Lee; Sang-Jun Park; Sunhwan Jo; Payal Chatterjee; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr.; Wonpil Im (J. Comput. Chem., 2022)

GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. - Mingtian Zhao; Abhishek A. Kognole; Sunhwan Jo; Aoxiang Tao; Anthony Hazel; Alexander D. MacKerell Jr. (J. Comput. Chem., 2023)