List of works by Wonpil Im

A conserved αβ transmembrane interface forms the core of a compact T-cell receptor-CD3 structure within the membrane

scientific article published on 10 October 2016

A novel strategy to determine protein structures using exclusively residual dipolar coupling.

scientific article

A repulsive electrostatic mechanism for protein export through the type III secretion apparatus

scientific article

A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties

scientific article

Activation mechanism of the mouse cold-sensing TRPM8 channel by cooling agonist and PIP <sub>2</sub>

scientific article published on 13 October 2022

Additive CHARMM36 Force Field for Nonstandard Amino Acids

scientific article published on 19 May 2021

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins ⬇️

scientific article published on November 1, 2003

An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins

scientific article

An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations

scientific article published on 21 September 2016

Analysis of Lipid Order States and Domains in Lipid Bilayer Simulations

scientific article published on 07 December 2018

Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors

scientific article published on 6 July 2012

Application of solid-state NMR restraint potentials in membrane protein modeling

scientific article published on 18 April 2008

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

scientific article

Assessing smectic liquid-crystal continuum models for elastic bilayer deformations

scientific article published on 21 January 2013

Automated builder and database of protein/membrane complexes for molecular dynamics simulations

scientific article

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

scientific article

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface

scientific article

Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction

scientific article published on 31 July 2020

Biophysical and functional characterization of Norrin signaling through Frizzled4

scientific article published on 13 August 2018

Brownian dynamics simulations of ion transport through the VDAC.

scientific article

CHARMM-GUI 10 years for biomolecular modeling and simulation

scientific article published on 14 November 2016

CHARMM-GUI <i>Ligand Designer</i> for Template-Based Virtual Ligand Design in a Binding Site

scientific article published on 10 November 2021

CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations

scientific article published on 22 July 2019

CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations

scientific article published on 28 October 2020

CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model

scientific article

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

scientific article

CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application

scientific article published on 20 December 2012

CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments

scientific article

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

scientific article published on 3 August 2017

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

scientific article published on 28 December 2018

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes

scientific article published on July 2009

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

scientific article

CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems

scientific article published on 01 March 2019

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems

scientific article published on 06 December 2021

CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations

scientific article published on 13 March 2014

CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers

scientific article published on 02 April 2021

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

scientific article published on 11 May 2017

CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems.

scientific article

CHARMM-GUI supports the Amber force fields

scientific article published on 01 July 2020

Calcium and hydroxyapatite binding site of human vitronectin provides insights to abnormal deposit formation

scientific article published on 22 July 2020

Challenges in structural approaches to cell modeling

scientific article published on 30 May 2016

Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes

scientific article published on 4 September 2017

Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies ⬇️

scientific article published on October 28, 2010

Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

scientific article published on 18 November 2019

Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers

scientific article

Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic

scientific article published on 17 February 2015

Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by Nuclear Magnetic Resonance Spectroscopy and Molecular Simulations.

scientific article published on 13 June 2017

Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions

scientific article published on 11 December 2015

Correction to “Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern”

scientific article published on 13 May 2022

De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein

scientific article published in March 2004

Design, solid-phase synthesis, and evaluation of a phenyl-piperazine-triazine scaffold as α-helix mimetics

scientific article

Differences in the Electrostatic Surfaces of the Type III Secretion Needle Proteins PrgI, BsaL, and MxiH

scientific article

Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

scientific article published on 03 December 2021

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies

scientific article published on 16 September 2021

Dynamics and Interactions of GPI-Linked lynx1 Protein with/without Nicotinic Acetylcholine Receptor in Membrane Bilayers

scientific article published on 09 April 2020

E. coli outer membrane and interactions with OmpLA.

scientific article

Effects of N-Glycan Composition on Structure and Dynamics of IgG1 Fc and Their Implications for Antibody Engineering

scientific article published on 4 October 2017

Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

scientific article

Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues

scientific article

Electrostatic free energy calculations using the generalized solvent boundary potential method

Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages

scientific article

Experimentally Guided Computational Methods Yield Highly Accurate Insights into Transmembrane Interactions within the T Cell Receptor Complex

scientific article published on 08 October 2020

Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination.

scientific article published in August 2007

G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures

scientific article

G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design

scientific article published on 27 January 2016

GS-align for glycan structure alignment and similarity measurement.

scientific article

Generalized born model with a simple smoothing function.

scientific article published in November 2003

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

scientific article

Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank.

scientific article

Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins

scientific article

Glycan fragment database: a database of PDB-based glycan 3D structures

scientific article

Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation

scientific article published in March 2017

Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model

scientific article published in March 2017

Heterogeneity in non-epitope loop sequence and outer membrane protein complexes alters antibody binding to the major porin protein PorB in serogroup B Neisseria meningitidis

scientific article published on 14 July 2017

How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?

scientific article published on July 2015

Identification of ligand templates using local structure alignment for structure-based drug design

scientific article

Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin

scientific article

Implicit solvation based on generalized Born theory in different dielectric environments

scientific article published in January 2004

Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations

scientific article published on 10 April 2020

Improving the CHARMM force field for polyunsaturated fatty acid chains.

scientific article

Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics

scientific article

Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature

scientific article published on November 2016

Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers

scientific article published on 3 April 2012

Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein

scientific article

Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes

scientific article published in Scientific Reports

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

scientific article

Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory.

scientific article

Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory

scientific article

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

scientific article

L-Met Activates Arabidopsis GLR Ca(2+) Channels Upstream of ROS Production and Regulates Stomatal Movement

scientific article published on December 2016

Langevin dynamics simulations of charged model phosphatidylinositol lipids in the presence of diffusion barriers: toward an atomic level understanding of corralling of PIP2 by protein fences in biological membranes

scientific article

Ligand binding site detection by local structure alignment and its performance complementarity

scientific article published on 4 September 2013

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

scientific article published on 18 December 2020

Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates

scientific article published on 14 October 2019

Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase

scientific article published on October 2014

Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding

scientific article published in Scientific Reports

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations

scientific article published on 3 November 2006

Membrane tension, lipid adaptation, conformational changes, and energetics in MscL gating

scientific article

Modeling and simulation of bacterial outer membranes and interactions with membrane proteins

scientific article

Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-Negative Porin

scientific article published on 01 July 2019

Molecular Basis of Aqueous-Like Activity of Lipase Treated with Glucose-Headed Surfactant in Organic Solvent

scientific article published on 14 November 2018

Molecular Simulation and Biochemical Studies Support an Elevator-type Transport Mechanism in EIIC.

scientific article published on 13 May 2017

Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics

scientific article

Molecular dynamics simulation strategies for protein-micelle complexes.

scientific article

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

scientific article

Molecular dynamics simulations of glycoproteins using CHARMM.

scientific article

Molecular dynamics studies of ion permeation in VDAC.

scientific article

Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers

scientific article published on 21 November 2013

NMR characterization of hydrophobic collapses in amyloidogenic unfolded states and their implications for amyloid formation

scientific article

NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes

scientific article

NMR-based simulation studies of Pf1 coat protein in explicit membranes

scientific article

Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function.

scientific article

Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions

scientific article

Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations

scientific article published on 22 April 2011

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

scientific article

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models

scientific article

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

scientific article

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

scientific article

Potential pharmacological chaperones targeting cancer-associated MCL-1 and Parkinson disease-associated α-synuclein

scientific article

Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins

scientific article published on 24 September 2015

Probing the U-shaped conformation of caveolin-1 in a bilayer

scientific article published on March 2014

Protein dynamics and ion traffic in bacterioferritin

scientific article published on 30 November 2012

Quantification of Drive-Response Relationships Between Residues During Protein Folding

scientific article published on August 2013

Quantitative Characterization of Cholesterol Partitioning between Binary Bilayers

scientific article published on 14 May 2018

Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation between Binary Bilayers

scientific article published on 14 October 2019

Refinement of NMR structures using implicit solvent and advanced sampling techniques

scientific article published in December 2004

Refinement of OprH-LPS Interactions by Molecular Simulations

scientific article

Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein

scientific article

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling

scientific article

Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation

scientific article

Role of hydrogen bonding and helix-lipid interactions in transmembrane helix association

scientific article published on 19 April 2008

Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies

scientific article published on 3 November 2015

Simulating Biomolecules: Festschrift to commemorate the 60th birthday of Charles L. Brooks III.

scientific article

Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes

Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes

scientific article published on April 2015

Solid-state NMR ensemble dynamics as a mediator between experiment and simulation

scientific article

Stalis: A Computational Method for Template-Based Ab Initio Ligand Design

scientific article published on 04 March 2019

Structural Conservation and Effects of Alterations in T Cell Receptor Transmembrane Interfaces

scientific article published on 29 January 2018

Structural basis of neuropeptide Y signaling through Y1 receptor

scientific article published on 14 February 2022

Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa

scientific article

The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport

scientific article

Theoretical and computational models of biological ion channels

scientific article

Theory of Adaptive Optimization for Umbrella Sampling

scientific article published on 12 June 2014

Transmembrane Motions of PglB Induced by LLO are Coupled with EL5 Loop Conformational Changes Necessary for OST Activity

scientific article

Transmembrane features governing Fc receptor CD16A assembly with CD16A signaling adaptor molecules.

scientific article published on 26 June 2017

Transmembrane helix assembly by window exchange umbrella sampling.

scientific article

Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables

scientific article

Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies

scientific article

Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly

scientific article published on 19 November 2012

U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids

scientific article published on 03 March 2019

Unfolding of a ClC chloride transporter retains memory of its evolutionary history.

scientific article published on 26 March 2018

Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores

scientific article

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