Generalized born model with a simple smoothing function. - Wonpil Im; Michael S. Lee; Charles L. Brooks III (J. Comput. Chem., 2003)

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. - Michael Feig; Alexey Onufriev; Michael S. Lee; Wonpil Im; David A. Case; Charles L. Brooks III (J. Comput. Chem., 2004)

Application of torsion angle molecular dynamics for efficient sampling of protein conformations. - Jianhan Chen; Wonpil Im; Charles L. Brooks III (J. Comput. Chem., 2005)

Implementation and application of helix-helix distance and crossing angle restraint potentials. - Jinhyuk Lee; Wonpil Im (J. Comput. Chem., 2007)

Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination. - Thenmalarchelvi Rathinavelan; Wonpil Im (J. Comput. Chem., 2007)

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

A novel strategy to determine protein structures using exclusively residual dipolar coupling. - Thenmalarchelvi Rathinavelan; 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)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. - Wonpil Im; Jinhyuk Lee; Taehoon Kim; Huan Rui (J. Comput. Chem., 2009)

Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance. - Jinhyuk Lee; Sihyun Ham; Wonpil Im (J. Comput. Chem., 2009)

Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. - Huan Rui; Wonpil Im (J. Comput. Chem., 2010)

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)

Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. - Hui Sun Lee; Wonpil Im (J. Chem. Inf. Model., 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)

Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity. - Hui Sun Lee; 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)

Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. - Pai-Chi Li; Naoyuki Miyashita; Wonpil Im; Satoshi Ishido; Yuji Sugita (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)

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)

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)

Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III. - Jonathan D. Hirst; Wonpil Im; Joan-Emma Shea (J. Comput. Chem., 2017)

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. - Pin-Chia Hsu; Bart M. H. Bruininks; Damien Jefferies; Paulo C. T. Souza; Jumin Lee; Dhilon S. Patel; Siewert J. Marrink; Yifei Qi; Syma Khalid; Wonpil Im (J. Comput. Chem., 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)

Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. - Hui Sun Lee; Wonpil Im (J. Comput. Chem., 2019)

U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids. - Soohyung Park; Kerney J. Glover; Wonpil Im (J. Comput. Chem., 2019)

CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems. - Yifei Qi; Jumin Lee; Jeffery B. Klauda; Wonpil Im (J. Comput. Chem., 2019)

GlyMDB: Glycan Microarray Database and analysis toolset. - Yiwei Cao; Sang-Jun Park; Akul Y. Mehta; Richard D. Cummings; Wonpil Im (Bioinform., 2020)

Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane. - Wonpil Im; Nilesh K. Banavali; Yun Lyna Luo (J. Comput. Chem., 2020)

CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations. - Yifei Qi; Jumin Lee; Xi Cheng; Rong Shen; Shahidul M. Islam; Benoît Roux; Wonpil Im (J. Comput. Chem., 2020)

Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. - Hugo Guterres; Wonpil Im (J. Chem. Inf. Model., 2020)

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. - Ya Gao 004; Jumin Lee; Iain Peter Shand Smith; Hwayoung Lee; Seonghoon Kim; Yifei Qi; Jeffery B. Klauda; Göran Widmalm; Syma Khalid; Wonpil Im (J. Chem. Inf. Model., 2021)

CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site. - Hugo Guterres; Sang-Jun Park; Yiwei Cao; Wonpil Im (J. Chem. Inf. Model., 2021)

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. - Hugo Guterres; Sang-Jun Park; Wei Jiang; Wonpil Im (J. Chem. Inf. Model., 2021)

CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement. - Hugo Guterres; Sang-Jun Park; Han Zhang 028; Wonpil Im (J. Chem. Inf. Model., 2021)

CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids. - Soohyung Park; Yeol Kyo Choi; Seonghoon Kim; Jumin Lee; Wonpil Im (J. Chem. Inf. Model., 2021)

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. - Han Zhang 028; Seonghoon Kim; Timothy J. Giese; Tai-Sung Lee; Jumin Lee; Darrin M. York; Wonpil Im (J. Chem. Inf. Model., 2021)

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)

Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes. - Irina D. Pogozheva; Grant A. Armstrong; Lingyang Kong; Timothy J. Hartnagel; Carly A. Carpino; Stephen E. Gee; Danielle M. Picarello; Amanda S. Rubin; Jumin Lee; Soohyung Park; Andrei L. Lomize; Wonpil Im (J. Chem. Inf. Model., 2022)

Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations. - Han Zhang 028; Seonghoon Kim; Wonpil Im (J. Chem. Inf. Model., 2022)

Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern. - Seonghan Kim; Yi Liu; Matthew Ziarnik; Sangjae Seo; Yiwei Cao; X. Frank Zhang; Wonpil Im (J. Comput. Chem., 2023)

Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides. - Ya Gao 004; Göran Widmalm; Wonpil Im (J. Chem. Inf. Model., 2023)

CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes. - Hugo Guterres; Wonpil Im (J. Chem. Inf. Model., 2023)

Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer. - Irina D. Pogozheva; Stanislav Cherepanov; Sang-Jun Park; Malini Raghavan; Wonpil Im; Andrei L. Lomize (J. Chem. Inf. Model., 2023)

Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods. - Han Zhang 028; Wonpil Im (J. Chem. Inf. Model., 2024)

Spontaneous curvature generation by peptides in asymmetric bilayers. - Soohyung Park; Amy Rice; Wonpil Im; Richard W. Pastor (J. Comput. Chem., 2024)

Substrates (Acyl-CoA and Diacylglycerol) Entry and Products (CoA and Triacylglycerol) Egress Pathways in DGAT1. - Hwayoung Lee; Wonpil Im (J. Comput. Chem., 2025)

CHARMM-GUI Bicelle Builder: An Extension of Membrane Builder for Modeling and Simulation of Bicelle Systems. - Seonghan Kim; Nathan R. Kern; Lauren Paolucci; Alan Jaemin Jo; Christopher P. Baryiames; D. Peter Tieleman; Linda Columbus; Wonpil Im (J. Chem. Inf. Model., 2025)