Wonpil Im

发表

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

Wei Jiang, Sunhwan Jo, Hui Sun Lee, 2013, J. Chem. Inf. Model..

Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors

Sunhwan Jo, Hui Sun Lee, Wonpil Im, 2012, J. Chem. Inf. Model..

CHARMM-GUI Ligand Reader & Modeler

Seonghoon Kim, Wonpil Im, Jumin Lee, 2017 .

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins

Alexander D. MacKerell, Sunhwan Jo, Wonpil Im, 2011, J. Comput. Chem..

Protegrin‐1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations

Wonpil Im, Huan Rui, W. Im, 2010, J. Comput. Chem..

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

Jonathan D. Hirst, Joan-Emma Shea, Wonpil Im, 2017, J. Comput. Chem..

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

Jumin Lee, Wonpil Im, Yifei Qi, 2017, J. Comput. Chem..

CHARMM-GUI Lecture Series on Molecular Modeling and Simulation

Krzysztof Kuczera, Jumin Lee, Wonpil Im, 2018 .

Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores

Sunhwan Jo, Benoît Roux, Wonpil Im, 2012, J. Comput. Chem..

Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Chaok Seok, Jumin Lee, Wonpil Im, 2020, bioRxiv : the preprint server for biology.

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

Generalized born model with a simple smoothing function

Charles L. Brooks, Wonpil Im, Michael S. Lee, 2003, J. Comput. Chem..

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

Sunhwan Jo, Benoît Roux, Wonpil Im, 2008, Nucleic Acids Res..

CHARMM-GUI: Brining Advanced Computational Techniques to Web Interface

Wonpil Im, Sunhwan Jo, 2010 .

Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

Hui Sun Lee, Wonpil Im, W. Im, 2013, J. Chem. Inf. Model..

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

Wonpil Im, Hui Sun Lee, W. Im, 2019, J. Comput. Chem..

CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations

Klaus Schulten, Xi Cheng, Wei Han, 2014, J. Chem. Inf. Model..

Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design

Hui Sun Lee, Wonpil Im, W. Im, 2012, J. Chem. Inf. Model..

CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems

Sunhwan Jo, Hui Sun Lee, Wonpil Im, 2013, J. Chem. Inf. Model..

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

Charles L. Brooks, Jianhan Chen, Wonpil Im, 2005, J. Comput. Chem..

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

Charles L. Brooks, David A. Case, Michael Feig, 2004, J. Comput. Chem..

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

Jumin Lee, Wonpil Im, Yifei Qi, 2019, J. Comput. Chem..

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

Wonpil Im, Thenmalarchelvi Rathinavelan, W. Im, 2008, J. Comput. Chem..

Computational Toolset for Glycoconjugate Modeling and Simulation

Sang-Jun Park, Jumin Lee, Wonpil Im, 2018 .

GlyMDB: Glycan Microarray Database and analysis toolset

Richard D Cummings, Wonpil Im, Sang-Jun Park, 2019, Bioinform..

CHARMM‐GUI: A web‐based graphical user interface for CHARMM

Taehoon Kim, Sunhwan Jo, Wonpil Im, 2008, J. Comput. Chem..

St-Analyzer: A Web-Based User Interface for Simulation Trajectory Analysis

Feng Chen, Wonpil Im, Sunhwan Jo, 2014 .

Beta‐hairpin restraint potentials for calculations of potentials of mean force as a function of beta‐hairpin tilt, rotation, and distance

Wonpil Im, Sihyun Ham, Jinhyuk Lee, 2009, J. Comput. Chem..

CHARMM‐GUI 10 years for biomolecular modeling and simulation

Alexander D. MacKerell, Xi Cheng, Sunhwan Jo, 2017, J. Comput. Chem..

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

Charles L. Brooks, Sunhwan Jo, Jumin Lee, 2017, J. Comput. Chem..

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

Wonpil Im, Thenmalarchelvi Rathinavelan, W. Im, 2007, J. Comput. Chem..

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

Taehoon Kim, Wonpil Im, Huan Rui, 2009, J. Comput. Chem..

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

Sunhwan Jo, Wonpil Im, W. Im, 2012, Nucleic Acids Res..

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

Pai-Chi Li, Yuji Sugita, Wonpil Im, 2014, J. Comput. Chem..

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Yiwei Cao, Chaok Seok, Sang-Jun Park, 2020, The journal of physical chemistry. B.

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

Wonpil Im, Hugo Guterres, W. Im, 2020, J. Chem. Inf. Model..

Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank

Sunhwan Jo, Jumin Lee, Hui Sun Lee, 2017, Bioinform..

Implementation and application of helix–helix distance and crossing angle restraint potentials

Wonpil Im, Jinhyuk Lee, W. Im, 2007, J. Comput. Chem..

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

Klaus Schulten, Jumin Lee, Wonpil Im, 2017, The journal of physical chemistry. B.

Theory of Adaptive Optimization for Umbrella Sampling

Wonpil Im, Soohyung Park, W. Im, 2014, Journal of chemical theory and computation.

ST‐analyzer: A web‐based user interface for simulation trajectory analysis

Feng Chen, Wonpil Im, Yifei Qi, 2014, J. Comput. Chem..

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Sunhwan Jo, Jooyoung Lee, Jumin Lee, 2019, Glycobiology.

Introduction of Membrane Analyzer and Updates of Membrane Builder

Wonpil Im, Sunhwan Jo, Jong Cheol Jeong, 2013 .

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

Benoît Roux, Wonpil Im, Jumin Lee, 2020, J. Comput. Chem..

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

Wonpil Im, Soohyung Park, Kerney J. Glover, 2019, J. Comput. Chem..

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

Sunhwan Jo, Jeffrey Skolnick, Hui Sun Lee, 2013, PLoS Comput. Biol..

Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane

Wonpil Im, Nilesh Banavali, Yun Lyna Luo, 2020, J. Comput. Chem..

CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations

Sunhwan Jo, Xi Cheng, Jumin Lee, 2014, J. Comput. Chem..

Glycan Structure Modeling and Simulation

Wonpil Im, 2019 .

GS-align for glycan structure alignment and similarity measurement

Sunhwan Jo, Jooyoung Lee, Jeffrey Skolnick, 2015, Bioinform..

CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement

Wonpil Im, Hugo Guterres, Sang-Jun Park, 2021, J. Chem. Inf. Model..

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides

Ya Gao, Wonpil Im, Jumin Lee, 2021, J. Chem. Inf. Model..

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

Wonpil Im, Wei Jiang, Hugo Guterres, 2020, J. Chem. Inf. Model..

CHARMM-GUI Ligand Designer for Template-Based Virtual Ligand Design in a Binding Site

Wonpil Im, Yiwei Cao, Hugo Guterres, 2021, J. Chem. Inf. Model..

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

Darrin M. York, Tai-Sung Lee, Wonpil Im, 2021, J. Chem. Inf. Model..

Electrostatic free energy calculations using the generalized solvent boundary potential method

Benoît Roux, Wonpil Im, Nilesh K. Banavali, 2002 .

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

Wonpil Im, Jumin Lee, Emad Tajkhorshid, 2015, Biophysical journal.

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field.

Helgi I Ingólfsson, Helgi I. Ingólfsson, Siewert J Marrink, 2015, Journal of chemical theory and computation.

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

Ansgar Philippsen, Wonpil Im, Daniel J Müller, 2002, Biophysical journal.

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

Wonpil Im, Taehoon Kim, W. Im, 2010, Biophysical journal.

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

Sunhwan Jo, Wonpil Im, Xi Cheng, 2013, Biophysical journal.

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

Sunhwan Jo, Olof Engström, Wonpil Im, 2013, Biophysical journal.

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

Wonpil Im, Huan Rui, W. Im, 2014, Biophysical journal.

Long-Ranged Protein-Glycan Interactions Stabilize Von Willebrand Factor A2 Domain from Mechanical Unfolding

Alparslan Oztekin, Wonpil Im, Jumin Lee, 2019, Biophysical Journal.

Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly.

Wonpil Im, W. Im, Soohyung Park, 2013, Journal of chemical theory and computation.

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

Sunhwan Jo, Wonpil Im, Taehoon Kim, 2012, Biochimica et biophysica acta.

Cholesterol flip-flop: insights from free energy simulation studies.

Sunhwan Jo, Wonpil Im, Huan Rui, 2010, The journal of physical chemistry. B.

Charmm-GUI Membrane Builder with Glycolipids and Lipopolysaccharides

Wonpil Im, Jumin Lee, Göran Widmalm, 2018 .

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

Wonpil Im, Yifei Qi, W. Im, 2015, Scientific Reports.

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

Wonpil Im, W. Im, Hui Sun Lee, 2016, Protein science : a publication of the Protein Society.

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

Wonpil Im, Xi Cheng, 2012, Biophysical journal.

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

Sunhwan Jo, Wonpil Im, Jumin Lee, 2018, Journal of chemical theory and computation.

Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms.

Wonpil Im, Kevin C. Song, Jeffery B. Klauda, 2014, The journal of physical chemistry. B.

Transmembrane helix assembly by window exchange umbrella sampling.

Wonpil Im, Taehoon Kim, W. Im, 2012, Physical review letters.

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

Wonpil Im, W. Im, Hui-Sun Lee, 2017, Scientific Reports.

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

Yuji Sugita, Michael Feig, Wonpil Im, 2019, Proceedings of the National Academy of Sciences.

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria.

Wonpil Im, Göran Widmalm, Seonghoon Kim, 2016, Biophysical journal.

E. coli outer membrane and interactions with OmpLA.

Wonpil Im, Göran Widmalm, Jeffery B. Klauda, 2014, Biophysical journal.

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

Wonpil Im, Charles L Brooks, C. Brooks, 2007, Biophysical journal.

CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation

Wonpil Im, 2016 .

Molecular dynamics studies of ion permeation in VDAC.

Wonpil Im, Huan Rui, Kyu Il Lee, 2011, Biophysical journal.

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

Wonpil Im, W. Im, Hui-Sun Lee, 2017, Methods in molecular biology.

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

Wonpil Im, Jianhan Chen, Jinhyuk Lee, 2008, Journal of magnetic resonance.

Implicit solvation based on generalized Born theory in different dielectric environments.

Michael Feig, Wonpil Im, Charles L Brooks, 2004, The Journal of chemical physics.

Brownian dynamics simulations of ion transport through the VDAC.

Wonpil Im, Huan Rui, Kyu Il Lee, 2011, Biophysical journal.

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

Sunhwan Jo, Wonpil Im, W. Im, 2011, Biophysical journal.

Quantitative Characterization of Cholesterol Partitioning between Binary Bilayers.

Wonpil Im, W. Im, Soohyung Park, 2018, Journal of chemical theory and computation.

Generalized solvent boundary potential for computer simulations

Benoît Roux, Wonpil Im, W. Im, 1999 .

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

Alexander D. MacKerell, Sunhwan Jo, Benoît Roux, 2014, Advances in protein chemistry and structural biology.

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

Sunhwan Jo, Wonpil Im, Taehoon Kim, 2011, Biophysical journal.

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

Sunhwan Jo, Wonpil Im, Yifei Qi, 2015, Glycobiology.

Protein–protein interactions in actin–myosin binding and structural effects of R405Q mutation: A molecular dynamics study

Wonpil Im, W. Im, Yuemin Liu, 2006, Proteins.