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Wonpil Im
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2020 – today
- 2024
- [j53]Soohyung Park
, Amy Rice
, Wonpil Im
, Richard W. Pastor
:
Spontaneous curvature generation by peptides in asymmetric bilayers. J. Comput. Chem. 45(9): 512-522 (2024) - [j52]Han Zhang, Wonpil Im:
Ligand Binding Affinity Prediction for Membrane Proteins with Alchemical Free Energy Calculation Methods. J. Chem. Inf. Model. 64(14): 5671-5679 (2024) - 2023
- [j51]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): 594-601 (2023) - [j50]Ya Gao
, Göran Widmalm
, Wonpil Im
:
Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides. J. Chem. Inf. Model. 63(5): 1592-1601 (2023) - [j49]Hugo Guterres
, Wonpil Im
:
CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes. J. Chem. Inf. Model. 63(15): 4772-4779 (2023) - [j48]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): 5874-5895 (2023) - 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) - [j46]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): 1036-1051 (2022) - [j45]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): 6084-6093 (2022) - 2021
- [j44]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): 535-546 (2021) - [j43]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): 831-839 (2021) - [j42]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): 3744-3751 (2021) - [j41]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): 4145-4151 (2021) - [j40]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): 5192-5202 (2021) - [j39]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): 5336-5342 (2021) - 2020
- [j38]Yiwei Cao
, Sang-Jun Park, Akul Y. Mehta
, Richard D. Cummings, Wonpil Im
:
GlyMDB: Glycan Microarray Database and analysis toolset. Bioinform. 36(8): 2438-2442 (2020) - [j37]Wonpil Im, Nilesh K. Banavali, Yun Lyna Luo:
Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane. J. Comput. Chem. 41(5): 385-386 (2020) - [j36]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): 415-420 (2020) - [j35]Hugo Guterres
, Wonpil Im
:
Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. J. Chem. Inf. Model. 60(4): 2189-2198 (2020)
2010 – 2019
- 2019
- [j34]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): 893-899 (2019) - [j33]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): 1570-1577 (2019) - [j32]Hui Sun Lee, Wonpil Im
:
Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. J. Comput. Chem. 40(17): 1622-1632 (2019) - 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) - [j30]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): 1111-1113 (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) - [j27]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): 2354-2363 (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
- [j25]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): 300-308 (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) - [j19]Hui Sun Lee, Wonpil Im:
Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity. J. Chem. Inf. Model. 53(9): 2462-2470 (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) - [j14]Hui Sun Lee, Wonpil Im:
Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. J. Chem. Inf. Model. 52(10): 2784-2795 (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) - 2010
- [j12]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): 2859-2867 (2010)
2000 – 2009
- 2009
- [j11]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): 1334-1343 (2009) - [j10]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:
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30(10): 1545-1614 (2009) - [j9]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): 1622-1633 (2009) - 2008
- [j8]Thenmalarchelvi Rathinavelan, Wonpil Im:
A novel strategy to determine protein structures using exclusively residual dipolar coupling. J. Comput. Chem. 29(10): 1640-1649 (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) - 2007
- [j5]Jinhyuk Lee, Wonpil Im:
Implementation and application of helix-helix distance and crossing angle restraint potentials. J. Comput. Chem. 28(3): 669-680 (2007) - [j4]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): 1858-1864 (2007) - 2005
- [j3]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): 1565-1578 (2005) - 2004
- [j2]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): 265-284 (2004) - 2003
- [j1]Wonpil Im, Michael S. Lee, Charles L. Brooks III:
Generalized born model with a simple smoothing function. J. Comput. Chem. 24(14): 1691-1702 (2003)
Coauthor Index
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