Wonpil Im

56 papers Journal 56
YearRankTypeTitle / Venue / Authors
2026 J jnl
CHARMM-GUI Hybrid ML/MM Builder for Hybrid Machine Learning and Molecular Mechanical Modeling and Simulations.
J. Chem. Inf. Model.
Florence Szczepaniak, Donghyuk Suh, Wonpil Im
2025 J jnl
CHARMM-GUI
J. Chem. Inf. Model.
Seonghan Kim, Nathan R. Kern, Lauren Paolucci, Alan Jaemin Jo, Christopher P. Baryiames, D. Peter Tieleman, Linda Columbus, Wonpil Im
2025 J jnl
Substrates (Acyl-CoA and Diacylglycerol) Entry and Products (CoA and Triacylglycerol) Egress Pathways in DGAT1.
J. Comput. Chem.
Hwayoung Lee, Wonpil Im
2024 J jnl
Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods.
J. Chem. Inf. Model.
Han Zhang, Wonpil Im
2024 J jnl
Spontaneous curvature generation by peptides in asymmetric bilayers.
J. Comput. Chem.
Soohyung Park, Amy Rice, Wonpil Im, Richard W. Pastor
2023 J jnl
Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern.
J. Comput. Chem.
Seonghan Kim, Yi Liu, Matthew Ziarnik, Sangjae Seo, Yiwei Cao, X. Frank Zhang, Wonpil Im
2023 J jnl
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.
J. Chem. Inf. Model.
Hugo Guterres, Wonpil Im
2023 J jnl
Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides.
J. Chem. Inf. Model.
Ya Gao, Göran Widmalm, Wonpil Im
2023 J jnl
Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer.
J. Chem. Inf. Model.
Irina D. Pogozheva, Stanislav Cherepanov, Sang-Jun Park, Malini Raghavan, Wonpil Im, Andrei L. Lomize
2022 J jnl
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.
J. Comput. Chem.
Abhishek A. Kognole, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell Jr., Wonpil Im
2022 J jnl
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes.
J. Chem. Inf. Model.
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
2022 J jnl
Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations.
J. Chem. Inf. Model.
Han Zhang, Seonghoon Kim, Wonpil Im
2021 J jnl
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
J. Chem. Inf. Model.
Han Zhang, Seonghoon Kim, Timothy J. Giese, Tai-Sung Lee, Jumin Lee, Darrin M. York, Wonpil Im
2021 J jnl
CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement.
J. Chem. Inf. Model.
Hugo Guterres, Sang-Jun Park, Han Zhang, Wonpil Im
2021 J jnl
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site.
J. Chem. Inf. Model.
Hugo Guterres, Sang-Jun Park, Yiwei Cao, Wonpil Im
2021 J jnl
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids.
J. Chem. Inf. Model.
Soohyung Park, Yeol Kyo Choi, Seonghoon Kim, Jumin Lee, Wonpil Im
2021 J jnl
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides.
J. Chem. Inf. Model.
Ya Gao, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, Yifei Qi, Jeffery B. Klauda, Göran Widmalm, Syma Khalid, Wonpil Im
2021 J jnl
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.
J. Chem. Inf. Model.
Hugo Guterres, Sang-Jun Park, Wei Jiang, Wonpil Im
2020 J jnl
CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations.
J. Comput. Chem.
Yifei Qi, Jumin Lee, Xi Cheng, Rong Shen, Shahidul M. Islam, Benoît Roux, Wonpil Im
2020 J jnl
Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane.
J. Comput. Chem.
Wonpil Im, Nilesh K. Banavali, Yun Lyna Luo
2020 J jnl
GlyMDB: Glycan Microarray Database and analysis toolset.
Bioinform.
Yiwei Cao, Sang-Jun Park, Akul Y. Mehta, Richard D. Cummings, Wonpil Im
2020 J jnl
Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Hugo Guterres, Wonpil Im
2019 J jnl
CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems.
J. Comput. Chem.
Yifei Qi, Jumin Lee, Jeffery B. Klauda, Wonpil Im
2019 J jnl
Stalis: A Computational Method for Template-Based Ab Initio Ligand Design.
J. Comput. Chem.
Hui Sun Lee, Wonpil Im
2019 J jnl
U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids.
J. Comput. Chem.
Soohyung Park, Kerney J. Glover, Wonpil Im
2017 J jnl
CHARMM-GUI 10 years for biomolecular modeling and simulation.
J. Comput. Chem.
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
2017 J jnl
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.
J. Comput. Chem.
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
2017 J jnl
CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.
J. Comput. Chem.
Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L. Brooks III, Hui Sun Lee, Wonpil Im
2017 J jnl
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.
Bioinform.
Sang-Jun Park, Jumin Lee, Dhilon S. Patel, Hongjing Ma, Hui Sun Lee, Sunhwan Jo, Wonpil Im
2017 J jnl
Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III.
J. Comput. Chem.
Jonathan D. Hirst, Wonpil Im, Joan-Emma Shea
2015 J jnl
GS-align for glycan structure alignment and similarity measurement.
Bioinform.
Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee, Wonpil Im
2014 J jnl
CHARMM-GUI
J. Comput. Chem.
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
2014 J jnl
CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations.
J. Chem. Inf. Model.
Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, Wonpil Im
2014 J jnl
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers.
J. Comput. Chem.
Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido, Yuji Sugita
2014 J jnl
ST-analyzer: A web-based user interface for simulation trajectory analysis.
J. Comput. Chem.
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
2013 J jnl
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application.
J. Chem. Inf. Model.
Sunhwan Jo, Wei Jiang, Hui Sun Lee, Benoît Roux, Wonpil Im
2013 J jnl
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems.
J. Chem. Inf. Model.
Xi Cheng, Sunhwan Jo, Hui Sun Lee, Jeffery B. Klauda, Wonpil Im
2013 J jnl
Glycan fragment database: a database of PDB-based glycan 3D structures.
Nucleic Acids Res.
Sunhwan Jo, Wonpil Im
2013 J jnl
Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity.
J. Chem. Inf. Model.
Hui Sun Lee, Wonpil Im
2013 J jnl
Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling.
PLoS Comput. Biol.
Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im
2012 J jnl
Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors.
J. Chem. Inf. Model.
Hui Sun Lee, Sunhwan Jo, Hyun-Suk Lim, Wonpil Im
2012 J jnl
Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design.
J. Chem. Inf. Model.
Hui Sun Lee, Wonpil Im
2012 J jnl
Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores.
J. Comput. Chem.
Kyu Il Lee, Sunhwan Jo, Huan Rui, Bernhard Egwolf, Benoît Roux, Richard W. Pastor, Wonpil Im
2011 J jnl
Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins.
J. Comput. Chem.
Sunhwan Jo, Kevin C. Song, Heather Desaire, Alexander D. MacKerell Jr., Wonpil Im
2010 J jnl
Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations.
J. Comput. Chem.
Huan Rui, Wonpil Im
2009 J jnl
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance.
J. Comput. Chem.
Jinhyuk Lee, Sihyun Ham, Wonpil Im
2009 J jnl
CHARMM: The biomolecular simulation program.
J. Comput. Chem.
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, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, Victor Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
2009 J jnl
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function.
J. Comput. Chem.
Wonpil Im, Jinhyuk Lee, Taehoon Kim, Huan Rui
2008 J jnl
A novel strategy to determine protein structures using exclusively residual dipolar coupling.
J. Comput. Chem.
Thenmalarchelvi Rathinavelan, Wonpil Im
2008 J jnl
CHARMM-GUI: A web-based graphical user interface for CHARMM.
J. Comput. Chem.
Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im
2008 J jnl
PBEQ-Solver for online visualization of electrostatic potential of biomolecules.
Nucleic Acids Res.
Sunhwan Jo, Miklós Vargyas, Judit Vasko-Szedlar, Benoît Roux, Wonpil Im
2007 J jnl
Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination.
J. Comput. Chem.
Thenmalarchelvi Rathinavelan, Wonpil Im
2007 J jnl
Implementation and application of helix-helix distance and crossing angle restraint potentials.
J. Comput. Chem.
Jinhyuk Lee, Wonpil Im
2005 J jnl
Application of torsion angle molecular dynamics for efficient sampling of protein conformations.
J. Comput. Chem.
Jianhan Chen, Wonpil Im, Charles L. Brooks III
2004 J jnl
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.
J. Comput. Chem.
Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III
2003 J jnl
Generalized born model with a simple smoothing function.
J. Comput. Chem.
Wonpil Im, Michael S. Lee, Charles L. Brooks III