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Wonpil Im

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TOP 3
Kyu Ii Lee; Richard W Pastor; Olaf S Andersen; Wonpil Im
Assessing smectic liquid-crystal continuum models for elastic bilayer deformations.
Sunhwan Jo; Hui Sun Lee; Benoît Roux; Wei Jiang; Wonpil Im
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
Sunhwan Jo; Hui Sun Lee; Jeffrey Skolnick; Wonpil Im
Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

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All Publications

2013: Kyu Ii Lee; Richard W Pastor; Olaf S Andersen; Wonpil Im
Assessing smectic liquid-crystal continuum models for elastic bilayer deformations.
Chemistry and physics of lipids 2013;169():19-26.
2013: Sunhwan Jo; Hui Sun Lee; Benoît Roux; Wei Jiang; Wonpil Im
CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application.
Journal of chemical information and modeling 2013;53(1):267-77.
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 computational biology 2013;9(3):e1002946.
2013: Sunhwan Jo; Wonpil Im
Glycan fragment database: a database of PDB-based glycan 3D structures.
Nucleic acids research 2013;41(Database issue):D470-4.
2012: Huan Rui; Mario Rivera; Wonpil Im
Protein dynamics and ion traffic in bacterioferritin.
Biochemistry 2012;51(49):9900-10.
2012: Jeffery B Klauda; Viviana Monje; Taehoon Kim; Wonpil Im
Improving the CHARMM force field for polyunsaturated fatty acid chains.
The journal of physical chemistry. B 2012;116(31):9424-31.
2012: Xi Cheng; Wonpil Im
NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes.
Biophysical journal 2012;102(7):L27-9.
2012: Taehoon Kim; Kyu Il Lee; Phillip Morris; Richard W Pastor; Olaf S Andersen; Wonpil Im
Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers.
Biophysical journal 2012;102(7):1551-60.
2012: Soohyung Park; Taehoon Kim; Wonpil Im
Transmembrane helix assembly by window exchange umbrella sampling.
Physical review letters 2012;108(10):108102.
2011: Sunhwan Jo; Alexander D. Mackerell; Kevin C Song; Heather Desaire; Wonpil Im
Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins.
Journal of computational chemistry 2011;32(14):3135-41.
2011: Urszula Golebiewska; Sergio Grinstein; Wonpil Im; Jason G Kay; Thomas Masters; Richard W Pastor; Suzanne Scarlata; Stuart McLaughlin
Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages.
Molecular biology of the cell 2011;22(18):3498-507.
2011: Hahnbeom Park; Wonpil Im; Chaok Seok
Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies.
Biophysical journal 2011;100(12):2955-63.
2011: Taehoon Kim; Sunhwan Jo; Wonpil Im
Solid-state NMR ensemble dynamics as a mediator between experiment and simulation.
Biophysical journal 2011;100(12):2922-8.
2011: Sunhwan Jo; Wonpil Im
Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.
Biophysical journal 2011;100(12):2913-21.
2011: Kevin C Song; Philip W Livanec; Jeffery B Klauda; Krzysztof Kuczera; Robert C Dunn; Wonpil Im
Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations.
The journal of physical chemistry. B 2011;115(19):6157-65.
2011: Kyu Il Lee; huang rui; Richard W Pastor; Wonpil Im
Brownian dynamics simulations of ion transport through the VDAC.
Biophysical journal 2011;100(3):611-9.
2011: Huan Rui; Kyu Il Lee; Richard W Pastor; Wonpil Im
Molecular dynamics studies of ion permeation in VDAC.
Biophysical journal 2011;100(3):602-10.
2011: Ji Hoon Lee; Qi Zhang; Sunhwan Jo; Sergio C Chai; Misook Oh; Wonpil Im; Hua lu; Hyun-Suk Lim
Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions.
Journal of the American Chemical Society 2011;133(4):676-9.
2010: Huan Rui; Wonpil Im
Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations.
Journal of computational chemistry 2010;31(16):2859-67.
2010: Sunhwan Jo; Huan Rui; Joseph B Lim; Jeffery B Klauda; Wonpil Im
Cholesterol flip-flop: insights from free energy simulation studies.
The journal of physical chemistry. B 2010;114(42):13342-8.
2010: Grace Jepkorir; Juan Carlos Rodríguez; Huan Rui; Wonpil Im; Scott Lovell; Kevin P Battaile; Aileen Y Alontaga; Erik T Yukl; Pierre Moanne-Loccoz; Mario Rivera
Structural, NMR spectroscopic, and computational investigation of hemin loading in the hemophore HasAp from Pseudomonas aeruginosa.
Journal of the American Chemical Society 2010;132(28):9857-72.
2010: Taehoon Kim; Wonpil Im
Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation.
Biophysical journal 2010;99(1):175-83.
2010: Kwang Hun Lim; Partha Nagchowdhuri; Thenmalarchelvi Rathinavelan; Wonpil Im
NMR characterization of hydrophobic collapses in amyloidogenic unfolded states and their implications for amyloid formation.
Biochemical and biophysical research communications 2010;396(4):800-5.
2010: Thenmalarchelvi Rathinavelan; Lingling Zhang; Wendy L Picking; David D Weis; Roberto N De Guzman; Wonpil Im
A repulsive electrostatic mechanism for protein export through the type III secretion apparatus.
Biophysical journal 2010;98(3):452-61.
2009: Huan Rui; Jinhyuk Lee; Wonpil Im
Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers.
Biophysical journal 2009;97(3):787-95.
2009: Wonpil Im; Jinhyuk Lee; Taehoon Kim; Huan Rui
Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function.
Journal of computational chemistry 2009;30(11):1622-33.
2009: Sunhwan Jo; Joseph Lim; Jeffery B Klauda; Wonpil Im
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.
Biophysical journal 2009;97(1):50-8.
2009: Taehoon Kim; Jinhyuk Lee; Wonpil Im
Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes.
Proteins 2009;76(1):86-98.
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.
Journal of computational chemistry 2009;30(8):1334-43.
2008: Sunhwan Jo; Taehoon Kim; Vidyashankara G Iyer; Wonpil Im
CHARMM-GUI: a web-based graphical user interface for CHARMM.
Journal of computational chemistry 2008;29(11):1859-65.
2008: Thenmalarchelvi Rathinavelan; Wonpil Im
A novel strategy to determine protein structures using exclusively residual dipolar coupling.
Journal of computational chemistry 2008;29(10):1640-9.
2008: Sunhwan Jo; Miklos Vargyas; Judit Vasko-Szedlar; Benoît Roux; Wonpil Im
PBEQ-Solver for online visualization of electrostatic potential of biomolecules.
Nucleic acids research 2008;36(Web Server issue):W270-5.
2008: Jinhyuk Lee; Jianhan Chen; Charles L Brooks; Wonpil Im
Application of solid-state NMR restraint potentials in membrane protein modeling.
Journal of magnetic resonance (San Diego, Calif. : 1997) 2008;193(1):68-76.
2008: Jinhyuk Lee; Wonpil Im
Role of hydrogen bonding and helix-lipid interactions in transmembrane helix association.
Journal of the American Chemical Society 2008;130(20):6456-62.
2008: Sung Ho Park; Cheolho Cheong; Juliana Idoyaga; Jae Y Kim; Jae-Hoon Choi; Yoonkyung Do; Haekyung Lee; Jung Heon Jo; Yong-Seok Oh; Wonpil Im; Ralph M Steinman; Chae Gyu Park
Generation and application of new rat monoclonal antibodies against synthetic FLAG and OLLAS tags for improved immunodetection.
Journal of immunological methods 2008;331(1-2):27-38.
2008: Jinhyuk Lee; Wonpil Im
Transmembrane helix tilting: insights from calculating the potential of mean force.
Physical review letters 2008;100(1):018103.
2007: yu wang; Andrew N Ouellette; Chet W Egan; Thenmalarchelvi Rathinavelan; Wonpil Im; Roberto N De Guzman
Differences in the electrostatic surfaces of the type III secretion needle proteins PrgI, BsaL, and MxiH.
Journal of molecular biology 2007;371(5):1304-14.
2007: Thenmalarchelvi Rathinavelan; Wonpil Im
Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination.
Journal of computational chemistry 2007;28(11):1858-64.
2007: Jinhyuk Lee; Wonpil Im
Implementation and application of helix-helix distance and crossing angle restraint potentials.
Journal of computational chemistry 2007;28(3):669-80.
2007: Lintao Bu; Wonpil Im; Charles L Brooks
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.
Biophysical journal 2007;92(3):854-63.
2007: Sunhwan Jo; Taehoon Kim; Wonpil Im
Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
PloS one 2007;2(9):e880.
2006: Yuemin Liu; Megan Scolari; Wonpil Im; Hyung-June Woo
Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: a molecular dynamics study.
Proteins 2006;64(1):156-66.
2006: Jianhan Chen; Wonpil Im; Charles L Brooks
Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field.
Journal of the American Chemical Society 2006;128(11):3728-36.
2005: Jianhan Chen; Wonpil Im; Charles L Brooks
Application of torsion angle molecular dynamics for efficient sampling of protein conformations.
Journal of computational chemistry 2005;26(15):1565-78.
2005: Wonpil Im; Charles L Brooks
Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(19):6771-6.
2005: Wonpil Im; Jianhan Chen; Charles L Brooks
Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models.
Advances in protein chemistry 2005;72():173-98.
2005: Jianhan Chen; Hyung-Sik Won; Wonpil Im; H Jane Dyson; Charles L Brooks
Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling.
Journal of biomolecular NMR 2005;31(1):59-64.
2004: Jianhan Chen; Wonpil Im; Charles L Brooks
Refinement of NMR structures using implicit solvent and advanced sampling techniques.
Journal of the American Chemical Society 2004;126(49):16038-47.
2004: Sergei Yu Noskov; Wonpil Im; Benoît Roux
Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory.
Biophysical journal 2004;87(4):2299-309.
2004: Wonpil Im; Charles L Brooks
De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein.
Journal of molecular biology 2004;337(3):513-9.
2004: Benoît Roux; Toby Allen; Simon Bernèche; Wonpil Im
Theoretical and computational models of biological ion channels.
Quarterly reviews of biophysics 2004;37(1):15-103.
2004: Michael Feig; Alexey Onufriev; Michael S Lee; Wonpil Im; David A Case; Charles L Brooks
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures.
Journal of computational chemistry 2004;25(2):265-84.
2004: Michael Feig; Wonpil Im; Charles L Brooks
Implicit solvation based on generalized Born theory in different dielectric environments.
The Journal of chemical physics 2004;120(2):903-11.
2003: Wonpil Im; Michael S Lee; Charles L Brooks
Generalized born model with a simple smoothing function.
Journal of computational chemistry 2003;24(14):1691-702.
2003: Wonpil Im; Michael Feig; Charles L Brooks
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins.
Biophysical journal 2003;85(5):2900-18.
2002: Wonpil Im; Benoît Roux
Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory.
Journal of molecular biology 2002;322(4):851-69.
2002: Wonpil Im; Benoît Roux
Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution.
Journal of molecular biology 2002;319(5):1177-97.
2002: Ansgar Philippsen; Wonpil Im; Andreas Engel; Tilman Schirmer; Benoît Roux; Daniel J Müller
Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin.
Biophysical journal 2002;82(3):1667-76.
2000: Benoît Roux; Simon Bernèche; Wonpil Im
Ion channels, permeation, and electrostatics: insight into the function of KcsA.
Biochemistry 2000;39(44):13295-306.