Wonpil Im

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 27

Top Topics

Molecular Dynamics

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

Publications

Han Zhang, Wonpil Im
Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods. J. Chem. Inf. Model. 64 (14) (2024)
Soohyung Park, Amy Rice, Wonpil Im, Richard W. Pastor
Spontaneous curvature generation by peptides in asymmetric bilayers. J. Comput. Chem. 45 (9) (2024)
Seonghan Kim, Yi Liu, Matthew Ziarnik, Sangjae Seo, Yiwei Cao, X. Frank Zhang, Wonpil Im
Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern. J. Comput. Chem. 44 (4) (2023)
Ya Gao, Göran Widmalm, Wonpil Im
Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides. J. Chem. Inf. Model. 63 (5) (2023)
Irina D. Pogozheva, Stanislav Cherepanov, Sang-Jun Park, Malini Raghavan, Wonpil Im, Andrei L. Lomize
Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer. J. Chem. Inf. Model. 63 (18) (2023)
Hugo Guterres, Wonpil Im
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes. J. Chem. Inf. Model. 63 (15) (2023)
Han Zhang, Seonghoon Kim, Wonpil Im
Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations. J. Chem. Inf. Model. 62 (23) (2022)
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
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes. J. Chem. Inf. Model. 62 (4) (2022)
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) (2022)
Hugo Guterres, Sang-Jun Park, Han Zhang, Wonpil Im
CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement. J. Chem. Inf. Model. 61 (8) (2021)
Han Zhang, Seonghoon Kim, Timothy J. Giese, Tai-Sung Lee, Jumin Lee, Darrin M. York, Wonpil Im
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER. J. Chem. Inf. Model. 61 (9) (2021)
Soohyung Park, Yeol Kyo Choi, Seonghoon Kim, Jumin Lee, Wonpil Im
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids. J. Chem. Inf. Model. 61 (10) (2021)
Hugo Guterres, Sang-Jun Park, Yiwei Cao, Wonpil Im
CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site. J. Chem. Inf. Model. 61 (11) (2021)
Hugo Guterres, Sang-Jun Park, Wei Jiang, Wonpil Im
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. J. Chem. Inf. Model. 61 (1) (2021)
Ya Gao, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, Yifei Qi, Jeffery B. Klauda, Göran Widmalm, Syma Khalid, Wonpil Im
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. J. Chem. Inf. Model. 61 (2) (2021)
Hugo Guterres, Wonpil Im
Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. J. Chem. Inf. Model. 60 (4) (2020)
Wonpil Im, Nilesh K. Banavali, Yun Lyna Luo
Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane. J. Comput. Chem. 41 (5) (2020)
Yiwei Cao, Sang-Jun Park, Akul Y. Mehta, Richard D. Cummings, Wonpil Im
GlyMDB: Glycan Microarray Database and analysis toolset. Bioinform. 36 (8) (2020)
Yifei Qi, Jumin Lee, Xi Cheng, Rong Shen, Shahidul M. Islam, Benoît Roux, Wonpil Im
CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations. J. Comput. Chem. 41 (5) (2020)
Hui Sun Lee, Wonpil Im
Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. J. Comput. Chem. 40 (17) (2019)
Yifei Qi, Jumin Lee, Jeffery B. Klauda, Wonpil Im
CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems. J. Comput. Chem. 40 (7) (2019)
Soohyung Park, Kerney J. Glover, Wonpil Im
U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids. J. Comput. Chem. 40 (16) (2019)
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) (2017)
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) (2017)
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) (2017)
Pin-Chia Hsu, Bart M. H. Bruininks, Damien Jefferies, Paulo Cesar Telles de Souza, Jumin Lee, Dhilon S. Patel, Siewert J. Marrink, Yifei Qi, Syma Khalid, Wonpil Im
CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. J. Comput. Chem. 38 (27) (2017)
Jonathan D. Hirst, Wonpil Im, Joan-Emma Shea
Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III. J. Comput. Chem. 38 (15) (2017)
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) (2015)
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) (2014)
Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido, Yuji Sugita
Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. J. Comput. Chem. 35 (4) (2014)
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
toward realistic biological membrane simulations. J. Comput. Chem. 35 (27) (2014)
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) (2014)
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) (2013)
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)
Sunhwan Jo, Wonpil Im
Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Res. 41 (Database-Issue) (2013)
Hui Sun Lee, Wonpil Im
Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity. J. Chem. Inf. Model. 53 (9) (2013)
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) (2013)
Hui Sun Lee, Wonpil Im
Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. J. Chem. Inf. Model. 52 (10) (2012)
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) (2012)
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) (2012)
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) (2011)
Huan Rui, Wonpil Im
Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. J. Comput. Chem. 31 (16) (2010)
Wonpil Im, Jinhyuk Lee, Taehoon Kim, Huan Rui
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. J. Comput. Chem. 30 (11) (2009)
Jinhyuk Lee, Sihyun Ham, Wonpil Im
Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance. J. Comput. Chem. 30 (8) (2009)
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, V. 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
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Sunhwan Jo, Taehoon Kim, Vidyashankara G. Iyer, Wonpil Im
CHARMM-GUI: A web-based graphical user interface for CHARMM. J. Comput. Chem. 29 (11) (2008)
Thenmalarchelvi Rathinavelan, Wonpil Im
A novel strategy to determine protein structures using exclusively residual dipolar coupling. J. Comput. Chem. 29 (10) (2008)
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) (2008)
Jinhyuk Lee, Wonpil Im
Implementation and application of helix-helix distance and crossing angle restraint potentials. J. Comput. Chem. 28 (3) (2007)
Thenmalarchelvi Rathinavelan, Wonpil Im
Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination. J. Comput. Chem. 28 (11) (2007)
Jianhan Chen, Wonpil Im, Charles L. Brooks III
Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J. Comput. Chem. 26 (15) (2005)
Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J. Comput. Chem. 25 (2) (2004)
Wonpil Im, Michael S. Lee, Charles L. Brooks III
Generalized born model with a simple smoothing function. J. Comput. Chem. 24 (14) (2003)