Sunhwan Jo

发表

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

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

Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations

W. Im, Sunhwan Jo, Taehoon Kim, 2007, PloS one.

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

Jeffery B. Klauda, W. Im, Sunhwan Jo, 2009, Biophysical journal.

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

Alexander D. MacKerell, Justin A. Lemkul, Jeffery B. Klauda, 2015, Journal of chemical theory and computation.

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

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

Computational Studies of Glycan Conformations in Glycoproteins

Sunhwan Jo, 2013 .

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.

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

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

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

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

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

Alexander D. MacKerell, Jeffery B. Klauda, Nathan R Kern, 2014, Biophysical journal.

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

W. Im, Sunhwan Jo, Hua Lu, 2011, Journal of the American Chemical Society.

Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots).

S. K. Lakkaraju, A. MacKerell, Sunhwan Jo, 2020, Biochimica et biophysica acta. General subjects.

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

W. Im, Yifei Qi, Sunhwan Jo, 2015, Biophysical journal.

Molecular dynamics simulations of glycoproteins using CHARMM.

Alexander D. MacKerell, Sairam S. Mallajosyula, W. Im, 2015, Methods in molecular biology.

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..

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

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

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

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

CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations

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

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 and modeler for CHARMM force field generation of small molecules

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

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.

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

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

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

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

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..

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

Nathan R. Kern, Nathan R Kern, B. Brooks, 2021, Journal of chemical theory and computation.

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..

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

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

Lipopolysaccharide membrane building and simulation.

Alexander D. MacKerell, Jeffery B. Klauda, W. Im, 2015, Methods in molecular biology.

Exploring protein‐protein interactions using the site‐identification by ligand competitive saturation methodology

Alexander D. MacKerell, Sirish Kaushik Lakkaraju, Sunhwan Jo, 2019, Proteins.

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

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

Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating.

Sunhwan Jo, Benoît Roux, Jeffery B. Klauda, 2012, Biophysical journal.

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..

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

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

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Ivet Bahar, Sunhwan Jo, Benoît Roux, 2014, PLoS Comput. Biol..

GS-align for glycan structure alignment and similarity measurement

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

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

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

The Salmonella Type III Secretion System Inner Rod Protein PrgJ Is Partially Folded*

Sunhwan Jo, K. Kaur, J. Galán, 2012, The Journal of Biological Chemistry.

Computational Characterization of Antibody-Excipient Interactions for Rational Excipient Selection using the Site Identification by Ligand Competitive Saturation (SILCS)-Biologics Approach.

Alexander D. MacKerell, Sunhwan Jo, Sandeep Somani, 2020, Molecular pharmaceutics.

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

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

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..

CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Alexander D. MacKerell, Justin A. Lemkul, W. Im, 2021, J. Comput. Chem..

CHARMM‐GUI 10 years for biomolecular modeling and simulation

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

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Klaus Schulten, James C. Phillips, Sunhwan Jo, 2017, Journal of chemical theory and computation.

Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS).

A. MacKerell, Sunhwan Jo, Sandeep Somani, 2020, Journal of pharmaceutical sciences.

A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations

Wei Jiang, Sunhwan Jo, Sunhwan Jo, 2015, Comput. Phys. Commun..

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization

Alexander D. MacKerell, Wenbo Yu, Sirish Kaushik Lakkaraju, 2019, J. Chem. Inf. Model..

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.

B. Roux, Sunhwan Jo, Wei Jiang, 2018, The journal of physical chemistry. B.

Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water.

Alexander D. MacKerell, S. K. Lakkaraju, Sunhwan Jo, 2018, Journal of Chemical Theory and Computation.

String method for Protein-Protein Binding Free Energy Calculations.

Wei Jiang, Sunhwan Jo, Donghyuk Suh, 2019, 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..

Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation

Alexander D. MacKerell, Sunhwan Jo, Himanshu Goel, 2021, Chemical science.

Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations.

Sunhwan Jo, Donghyuk Suh, Ziwei He, 2016, The journal of physical chemistry. B.

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

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

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

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

GPU‐specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations

A. MacKerell, Sunhwan Jo, Mingtian Zhao, 2023, J. Comput. Chem..

Structural and thermodynamic framework for PIEZO1 modulation by small molecules

Sunhwan Jo, Han Zhang, Jérôme J. Lacroix, 2023, Proceedings of the National Academy of Sciences of the United States of America.