Wonpil Im
Research Group
About PI Publications Members Teaching Funding Home


  1. E. Luna, S. Kim, Y. Gao, G. Widmalm, and W. Im
    Molecular Simulation Studies of Vibrio cholerae O1 LPS Symmetric Bilayers Elucidate Properties of Different Lipid A Types.
    in preparation
  1. D.S. Patel, P. Morales, G. Widmalm, and W. Im
    Molecular Dynamics and NMR Spectroscopy Studies of Escherichia coli O176 Lipopolysaccharide Structure and Dynamics.
    in preparation
  1. C. Singh, H. Lee, Y. Tian, L.M. Fujimoto, Y. Yao, S.A. Ivanov, R.Z. Shaikhutdinova, A.P. Asinimov, W. Im, and F.M. Marassi
    Specific Interaction of Yersinia pestis Ail with Outer Membrane Lipopolysaccharide..
    in preparation
  1. C. Dong, K.R. Anderson, X.F. Zhang, J.M. Miwa, and W. Im
    Dynamics and Interactions of GPI-Linked Lynx1 Protein with/without Nicotinic Acetylcholine Receptor in Membrane Bilayers.
    in preparation
  1. W. Im and S. Khalid
    Molecular Simulations of Bacterial Membranes Come of Age.
  1. K.R. Anderson, H-X. Wang, K.L. Feuer, W-P. Cao, H.S. Lee, K.J. McLaughlin, A. Hupbach, W. Im, X.F. Zhang, J.M. Miwa
    A Pharmacogenetic Approach to Targeting Anxiety: Implications for Lynx2-based Plasticity.
  1. C. Wang, S. Qiao, S. Yu, L. Chen, S. Kim, K. Wang, Q. Luo, J. Zheng, Y. Zhang, F. Wu, X. Lei, J. Lou, M. Hennig, W. Im, M. Zhou, L. Miao, and Y. Huang
    Structure and Mechanism of Lipoprotein Transport to the Cell Surface via the Lipopolysaccharide Translocon in Gram-negative Bacteria.
  1. Y. Cao, S-J. Park, A.Y. Mehta, R.D. Cummings, and W. Im
    GlyMDB: Glycan Microarray Database and Analysis Toolset.
    Bioinformatics in press (2019)
  1. G. Nawrocki, W. Im, Y. Sugita, and M. Feig
    Clustering and Dynamics of Crowded Proteins near Membranes and Their Influence on Membrane Bending.
    Proc. Natl. Acad. Sci. USA in press (2019)
  1. Y. Gao, J. Lee, G. Widmalm, and W. Im
    Preferred Conformations of Lipooligosaccharides and Oligosaccharides of Moraxella catarrhalis.
    Glycobiology in press (2019)
  1. S. Park, M.S. Yeom, O.S. Andersen, R.W. Pastor, and W. Im
    Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation Between Binary Bilayers.
    J. Chem. Theory Comput. in press (2019)
  1. H. Guterres, H.S. Lee, and W. Im
    Ligand Binding Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.
    J. Chem. Theory Comput. in press (2019)
  1. Y. Qi, J. Lee, X. Cheng, R. Shen, S.M. Islam, B. Roux, and W. Im
    CHARMM-GUI DEER Facilitator for Spin-pair Distance Distribution Calculations and Preparation of Restrained-Ensemble Molecular Dynamics Simulations.
    J. Comput. Chem. in press (2019)
  1. C. Dong, S. Kania, M. Morabito, X.F. Zhang, W. Im, A. Oztekin, X. Cheng, and E.B. Webb III
    A Mechano-Reactive Coarse-Grained Model of the Blood Clotting Agent von Willebrand Factor.
    J. Chem. Phys. 151:124905 (2019)
  1. A. Kesireddy, K.R. Pothula, J. Lee, D.S. Patel, M. Pathania, B. van den Berg, W. Im, and U. Kleinekathöfer
    Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-negative Porin.
    J. Phys. Chem. B. 123:5700-5708 (2019)
  1. H.S. Lee and W. Im
    Stalis: A Computational Method for Template-based Ab Initio Ligand Design.
    J. Comput. Chem. 40:1622-1632 (2019)
  1. S. Park, K.J. Glover, and W. Im
    U-shaped Caveolin-1 Conformations are Tightly Regulated by Hydrogen Bonds with Lipids.
    J. Comput. Chem. 40:1570-1577 (2019)
  1. A.V. Hughes, D.S. Patel, G. Widmalm, J.B. Klauda, L.A Clifton, and W. Im
    Physical Properties of Gram-negative Bacterial Outer Membranes: Neutron Reflectometry and Molecular Simulation.
    Biophys. J. 116:1095-1104 (2019)
  1. S-J. Park, J. Lee, Y. Qi, N.R. Kern, H.S. Lee, S. Jo, IS Joung, K. Joo, J. Lee, and W. Im
    CHARMM-GUI Glycan Modeler for Modeling and Simulation of Carbohydrates and Glycoconjugates.
    Glycobiology 29:320-331 (2019)
  1. Y. Qi, J. Lee, J.B. Klauda, and W. Im
    CHARMM-GUI Nanodisc Builder for Modeling and Simulation of Various Nanodisc Systems.
    J. Comput. Chem. 40:893-899 (2019)
  1. J. Lee, D.S. Patel, J. Ståhle, S-J. Park, N.R. Kern, S. Kim, J. Lee, X. Cheng, M.A. Valvano, O. Holst, Y. Knirel, Y. Qi, S. Jo, J.B. Klauda, G. Widmalm, and W. Im
    CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.
    J. Chem. Theory Comput. 15:775-786 (2019)
  1. S. Park and W. Im
    Analysis of Lipid Order States and Domains in Lipid Bilayer Simulations.
    J. Chem. Theory Comput. 15:688-697 (2019)  [cover]
  1. S. Kim, M.M. Pires, and W. Im
    Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes.
    Sci. Rep. 8:17704 (2018)
  1. H.S. Lee, Y. Oh, M-J. Kim, and W. Im
    Molecular Basis of Aqueous-like Activity of Lipase Treated with Glucose-headed Surfactant in Organic Solvent.
    J. Phys. Chem. B. 122:10659-10668 (2018)
  1. C. Dong, J. Lee, S. Kim, W. Lai, E.B. Webb III, A. Oztekin, X.F. Zhang, and W Im
    Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding.
    Sci. Rep. 8:16017 (2018)
  1. M.J. Sabulski, S. Kim, S.E. Pidgeon, Y. Yu, D.S. Patel, S. Regen, W. Im, and M.M. Pires
    Synthetic Immunotherapeutics Against Gram-negative Pathogens.
    Cell Chem. Biol. 25:1185-1194.e5 (2018)
  1. J. Lee, K.R. Pothula, U. Kleinekathöfer, and W. Im
    Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes.
    J. Phys. Chem. B. 122:8185-8192 (2018)
  1. I. Bang, H.R. Kim, A. Beaven, J. Kim, S. Ko, G.R. Lee, W. Im, C. Seok, K.Y. Chung, and H-J. Choi
    Biophysical and Functional Characterization of Norrin Signaling through Frizzled4.
    Proc. Natl. Acad. Sci. USA 115:8787-8792 (2018)
  1. N.I. Nissen, K.R. Anderson, H. Wang, H.S. Lee, C. Garrison, S.A. Eichelberger, K. Ackerman, W. Im, and J.M. Miwa
    Augmenting the Antinociceptive Effects of Nicotinic Acetylcholine Receptor Activity through Lynx1 Modulation.
    PLoS ONE 13:e0199643 (2018)
  1. S. Park and W. Im
    Quantitative Characterization of Cholesterol Partitioning Between Binary Bilayers.
    J. Chem. Theory Comput. 14:2829-2833 (2018)
  1. Z. Ren, J. Lee, Y Nian, L Hu, Z Xu, J.G. McCoy, A. Ferreon, W. Im, and M. Zhou
    Structure of an EIIC Sugar Transporter Trapped in an Inward-facing Conformation.
    Proc. Natl. Acad. Sci. USA 115:5962-5967 (2018)
  1. D. Min, R.E. Jefferson, Y. Qi, J.Y. Wang, M.A. Arbing, W. Im, and J.U. Bowie
    Folding of ClC Chloride Transporter Retains Memory of Its Evolutionary History.
    Nat. Chem. Biol. 14:489-496 (2018)
  1. S. Park, L. Krshnan, M.J. Call, M.E. Call, and W. Im
    Structural Conservation and Effects of Alterations in T Cell Receptor Transmembrane Interfaces.
    Biophys. J. 114:1030-1035 (2018)  [featured in NEW AND NOTABLE]
  1. S. Jo, D. Myatt, Y. Qi, J. Doutch, L.A Clifton, W. Im, and G. Widmalm
    Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study.
    J. Phys. Chem. B. 122:1169-1175 (2018)
  1. A.H. Beaven, A.J. Sodt, R.W. Pastor, R.E. Koeppe II, O.S. Andersen, and W. Im
    Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes.
    J. Chem. Theory Comput. 13:5054-5064 (2017)
  1. H.S. Lee and W. Im
    Effects of N-Glycan Composition on Structure and Dynamics of IgG1 Fc and Their Implications for Antibody Engineering.
    Sci. Rep. 7:12659 (2017)
  1. S-J. Park, J. Lee, D.S. Patel, H. Ma, H.S. Lee, S. Jo, and W. Im
    Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank.
    Bioinformatics 19:3051-3057 (2017)
  1. A. Machen, N. Akkaladevi, P. O'Neil, C. Trecazzi, S. Mukherjee, Y. Qi, R. Dillard, W. Im, D. Patel, B.L. Pentelute, J. Collier, T.A. White, E.P Gogol, and M.T. Fisher
    Anthrax Toxin Pore Formation and Asymmetric Cryo-EM Structure of LFN Bound PA Pore.
    Toxins 9:298 (2017)
  1. K.A. Matthias, M.B Strader, H.F. Nawar, J. Lee, D.S. Patel, W. Im, M.C. Bash
    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.
    Mol. Microbiol. 105:934-953 (2017)  [cover]
  1. P.C. Hsu, B. Bruininks, D. Jefferies, P.T. de Souza, J. Lee, D.S. Patel, S.J. Marrink, Y. Qi, S. Khalid, and W. Im
    CHARMM-GUI Martini Maker for Modeling and Simulation of Complex Bacterial Membranes with Lipopolysaccharides.
    J. Comput. Chem. 38:2354-2363 (2017)  [cover]
  1. P. Morales, D.S. Patel, O. Engström, W. Im, and G. Widmalm
    Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by NMR Spectroscopy and Molecular Simulations.
    Biochemistry 56:3826-3839 (2017)
  1. A. Blázquez-Moreno, S. Park, W. Im, M.J. Call, M.E. Call, and H.T. Reyburn
    Transmembrane Features Governing Fc Receptor CD16A Assembly with CD16A Signaling Adaptor Molecules.
    Proc. Natl. Acad. Sci. USA 114:E5645-E5654 (2017)
  1. H.S. Lee and W. Im
    Transmembrane Motions of PglB Induced by LLO are Coupled with EL5 Loop Conformational Changes Necessary for OST Activity.
    Glycobiology 27:734-742 (2017)
  1. S. Kim, J. Lee, S. Jo, C.L. Brooks III, H.S. Lee, and W. Im
    CHARMM-GUI Ligand Reader and Modeler for CHARMM Force Field Generation of Small Molecules.
    J. Comput. Chem. 38:1879-1886 (2017)
  1. J. Lee, Z. Ren, M. Zhou, and W. Im
    Molecular Simulation and Biochemical Studies Support an Elevator-Type Transport Mechanism in EIIC.
    Biophys. J. 112:2249-2252 (2017)
  1. S. Jo, X. Cheng, J. Lee, S. Kim, S-J. Park, D.S. Patel, A.H. Beaven, K.I. Lee, H. Rui, S. Park, H.S. Lee, B. Roux, A.D. MacKerell Jr, J.B. Klauda, Y. Qi, and W. Im
    CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation.
    J. Comput. Chem. 38:1114-1124 (2017)
  1. Y. Qi, J. Lee, A. Singharoy, R. Mcgreevy, K. Schulten, and W. Im
    CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.
    J. Phys. Chem. B. 121:3718-3723 (2017)
  1. D.S. Patel, Y. Qi, and W. Im
    Modeling and Simulation of Bacterial Outer Membranes and Interactions with Membrane Proteins.
    Curr. Opin. Struct. Biol. 43:131-140 (2017)
  1. A.J. Sodt, A.H. Beaven, O.S. Andersen, W. Im, and R.W. Pastor
    Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model.
    Biophys. J. 112:1198-1213 (2017)
  1. A.H. Beaven, A.M. Maer, A.J. Sodt, H. Rui, R.W. Pastor, O.S. Andersen, and W. Im
    Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation.
    Biophys. J. 112:1185-1197 (2017)
  1. J. Lee, D.S. Patel, I. Kucharska, L.K. Tamm, and W. Im
    Refinement of OprH-LPS Interactions by Molecular Simulations.
    Biophys. J. 112:346-355 (2017)
  1. D. Kong, H-C. Hu, E. Okuma, Y. Lee, H.S. Lee, S. Munemasa, D. Cho, L. Pedoeim, B. Rodriguez, C. Ju, W. Im, Y. Murara, Z-M. Pei, and J. M. Kwak
    L-Met Activates Arabidopsis GLR Ca2+ Channels Upstream of ROS and Regulates Stomatal Movement.
    Cell reports 17:2553-2561 (2016)
  1. C.T. Boughter, V. Monje-Galvan, W. Im, and J.B. Klauda
    Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics.
    J. Phys. Chem. B. 120:11761-11772 (2016)
  1. D.S. Patel, S. Park, E.L. Wu, M.S. Yeom, G. Widmalm, J.B. Klauda, and W. Im
    Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature.
    Biophys. J. 111:1987-1999 (2016)
  1. L. Krshnan, S. Park, W. Im, M.J. Call, and M.E. Call
    A Conserved αβ Transmembrane Interface Forms the Core of a Compact T Cell Receptor-CD3 Structure Within the Membrane.
    Proc. Natl. Acad. Sci. USA 113:E6649-E6658 (2016)
  1. S. Kim, D.S. Patel, S. Park, J. Slusky, J.B. Klauda, G. Widmalm, and W. Im
    Bilayer Properties of Lipid A from Various Gram-negative Bacteria.   [News Article]
    Biophys. J. 111:1750-1760 (2016)
  1. Y. Qi, J.B. Klauda, and W. Im
    Effects of Spin-labels on Membrane Burial Depth of MARCKS-ED Residues.
    Biophys. J. 111:1600-1603 (2016)
  1. X. Zhuang, E.M. Dávila-Contreras, A.H. Beaven, W. Im, and J.B. Klauda
    An Extensive Simulation Study of Lipid Bilayer Properties with Different Head Groups, Acyl Chain Lengths, and Chain Saturations.
    Biochimica et Biophysica Acta (BBA) - Biomembranes 1858:3093-3104 (2016)
  1. W. Im, J. Liang, A. Olson, H-X. Zhou, S. Vajda, and I. Vakser
    Challenges in Structural Approaches to Cell Modeling.
    J. Mol. Biol. 428:2943-2964 (2016)
  1. P.J. Fleming, D.S. Patel, E.L. Wu, Y. Qi, M.S. Yeom, M.C. Sousa, K.G. Fleming, and W. Im
    BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.
    Biophys. J. 110:2698-2709 (2016)
  1. J.G. McCoy, Z. Ren, V. Stanevich, J. Lee, S. Mitra, E.J. Levin, S. Poget, M. Quick, W. Im, and M. Zhou
    The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight Into the Elevator Mechanism of Membrane Transport.
    Structure 24:956-964 (2016)
  1. T. Mori, N. Miyashita, W. Im, M. Feig, and Y. Sugita
    Molecular Dynamics Simulations of Biological Membranes and Membrane Proteins Using Enhanced Conformational Sampling Algorithms.
    Biochimica et Biophysica Acta (BBA) - Biomembranes 1858:1635-1651 (2016)
  1. X. Cheng, J-K. Kim, Y. Kim, J.U. Bowie, and W. Im
    Molecular Dynamics Simulation Strategies for Protein-Micelle Complexes.
    Biochimica et Biophysica Acta (BBA) - Biomembranes 1858:1566-1572 (2016)
  1. R. Kumar, Y. Qi, H. Matsumura, S. Lovell, H. Yao, K.P. Battaile, W. Im, P. Moënne-Loccoz, and M Rivera
    Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein.
    Biochemistry 55:2622-2631 (2016)
  1. H.S. Lee and W. Im
    G-LoSA: An Efficient Computational Tool for Local Structure-Centric Biological Studies and Drug Design.
    Protein Sci. 25:865-876 (2016)
  1. Y. Qi, S. Jo, and W. Im
    Roles of Glycans in Interactions Between gp120 and HIV Broadly Neutralizing Antibodies.
    Glycobiology 26:251-260 (2016)
  1. D.S. Patel, S. Re, E.L. Wu, Y. Qi, P.E. Klebba, G. Widmalm, M.S. Yeom, Y. Sugita, and W. Im
    Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.
    Biophys. J. 110:930-938 (2016)
  1. J. Lee, X. Cheng, J.M. Swails, M.S. Yeom, P. Eastman, J. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V.S. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell Jr, J.B. Klauda, and W. Im
    CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field.
    J. Chem. Theory Comput. 12:405-413 (2016)
  1. J.H. Lee, M. Oh, H.S. Kim, H.S. Lee, W. Im, and H-S. Lim
    Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions.
    ACS Comb. Sci. 18:36-42 (2016)
  1. S. Jo, Y. Qi, and W. Im
    Preferred Conformations of N-glycan Core Pentasaccharide in Solution and in Glycoproteins.
    Glycobiology 26:19-29 (2016)
  1. E.L. Wu, Y. Qi, S. Park, S.S. Mallajosyula, A.D. MacKerell, Jr., J.B. Klauda, and W. Im
    Insight into Early-stage Unfolding of GPI-anchored Human Prion Protein.
    Biophys. J. 109:2090-2100 (2015)
  1. Y. Qi, X. Cheng, J. Lee, J.V. Vermaas, T.V. Pogorelov, E. Tajkhorshid, S. Park, J.B. Klauda, and W. Im
    CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model.
    Biophys. J. 109:2012-2022 (2015)
  1. Y. Qi, H.I. Ingólfsson, X. Cheng, J. Lee, S.J. Marrink, and W. Im
    CHARMM-GUI Martini Maker for Coarse Grained Simulations with the Martini Force Field.
    J. Chem. Theory Comput. 11:4486-4494 (2015)
  1. S. Park, A.H. Beaven, J.B. Klauda, and W. Im     [100th paper]
    How Tolerant are Membrane Simulations with Mismatch in Area per Lipid Between Leaflets?
    J. Chem. Theory Comput. 11:3466-3477 (2015)
  1. K. Knoblich, S. Park, M. Lutfi, L. van 't Hag, C.E. Conn, S.A. Seabrook, J. Newman, P.E. Czabotar, W. Im, M.E. Call and M.J. Call
    Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly.
    Cell reports 11:1184-1192 (2015)
  1. H.S. Lee, S. Jo, S. Mukherjee, S-J. Park, J. Skolnick, J. Lee, and W. Im
    GS-align for Glycan Structure Alignment and Similarity Measurement.   [GS-align website]
    Bioinformatics 31:2653-2659 (2015)
  1. X. Cheng, S. Jo, Y. Qi, F.M. Marassi, and W. Im
    Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes.
    Biophys. J. 108:1954-1962 (2015)
  1. H.S. Lee, C. Seok, and W. Im
    Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy.
    J. Chem. Theory Comput. 11:1255-1266 (2015)
  1. H.S. Lee, Y. Qi, and W. Im
    Effects of N-glycosylation on Protein Conformation and Dynamics: Protein Data Bank Analysis and Molecular Dynamics Simulation Study.
    Sci. Rep. 5:8926 (2015)
  1. H. Yao, H. Rui, R. Kumar, K. Eshelman, S. Lovell, K.P. Battaile, W. Im, and M. Rivera
    Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic.
    Biochemistry 54:1611-1627 (2015)
  1. W.S. Lee, H-J. Moon, M. Oh, H.S. Lee, J.H. Lee, W. Im, and H-S. Lim
    Design, Solid-Phase Synthesis, and Evaluation of a Phenyl-Piperazine-Triazine Scaffold as α-Helix Mimetics.
    ACS Comb. Sci. 16:695-701 (2014)
  1. K.I. Lee, W. Im, and R.W. Pastor
    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.
    BMC Biophys. 7:13 (2014)
  1. N.R. Kern, H.S. Lee, E.L. Wu, S. Park, K. Vanommeslaeghe, A.D. MacKerell, Jr., J.B. Klauda, S. Jo, and W. Im
    Lipid-Linked Oligosaccharides in Membranes Sample Conformations that Facilitate Binding to Oligosaccharyltransferase.
    Biophys. J. 107:1885-1895 (2014)
  1. S. Jo, X. Cheng, S.M. Islam, L. Huang, H. Rui, A. Zhu, H.S. Lee, Y. Qi, W. Han, K. Vanommeslaeghe, A.D. MacKerell, Jr., B. Roux, and W. Im
    CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues.
    Adv. Protein Chem. Struct. Biol. 96:235-265 (2014)
  1. E.L. Wu, X. Cheng, S. Jo, H. Rui, K.C. Song, E.M. Dávila-Contreras, Y. Qi, J. Lee, V. Monje-Galvan, R.M. Venable, J.B. Klauda, and W. Im
    CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations.
    J. Comput. Chem. 35:1997-2004 (2014)  [cover]
  1. M. Oh, J.H. Lee, W. Wang, H.S. Lee, W.S. Lee, C. Burlak, W. Im, Q.Q. Hoang, and H-S. Lim
    Potential Pharmacological Chaperones Targeting Cancer-associated MCL-1 and Parkinson's Disease-associated α-synuclein.
    Proc. Natl. Acad. Sci. USA 111, 11007-11012 (2014)
  1. X. Zhuang, J. Makover, W. Im, and J.B. Klauda
    A Systematic Molecular Dynamics Simulation Study of Temperature Dependent Bilayer Structural Properties.
    Biochimica et Biophysica Acta (BBA) - Biomembranes 10:2520-2529 (2014)
  1. S. Park and W. Im
    Theory of Adaptive Optimization for Umbrella Sampling.
    J. Chem. Theory Comput. 10:2719-2728 (2014)
  1. E.L. Wu, P. Fleming, M.S. Yeom, G. Widmalm, J.B. Klauda, K.G. Fleming, and W. Im
    E. coli Outer Membrane and Interactions with OmpLA.
    Biophys. J. 106:2493-2502 (2014)  [cover]
  1. E.L. Wu, Y. Qi, K.C. Song, J.B. Klauda, and W. Im
    Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms.
    J. Phys. Chem. B. 118:4315-4325 (2014)
  1. J.C. Jeong, S. Jo, E.L. Wu, Y. Qi, V. Monje-Galvan, M.S. Yeom, L. Gorenstein, F. Chen, J.B. Klauda, and W. Im
    ST-analyzer: A Web-based User Interface for Simulation Trajectory Analysis.   [ST-analyzer website]
    J. Comput. Chem. 35:957-996 (2014)  [cover]
  1. Y. Qi, X. Cheng, W. Han, S. Jo, K. Schulten, and W. Im
    CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations.
    J. Chem. Inf. Model. 54:1003-1009 (2014)
  1. H. Rui, K.T. Root, J. Lee, K.J. Glover, and W. Im
    Probing the U-shaped Conformation of Caveolin-1 in a Bilayer.
    Biophys. J. 106:1371-1380 (2014)
  1. P-C. Li, N. Miyashita, W. Im, S. Ishido, and Y. Sugita
    Multidimensional Umbrella Sampling and Replica-Exchange Molecular Dynamics Simulations for Structure Prediction of Transmembrane Helix Dimers.
    J. Comput. Chem. 35:300-308 (2014)
  1. H.S. Lee and W. Im
    Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity.   [G-LoSA website]
    J. Chem. Inf. Model. 53:2462-2470 (2013)
  1. E.L. Wu, O. Engström, S. Jo, D. Stuhlsatz, M.S. Yeom, J.B. Klauda, G. Widmalm, and W. Im
    Molecular Dynamics Simulation and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics.
    Biophys. J. 105:1444-1455 (2013)
  1. X. Cheng, S. Jo, H.S. Lee, J.B. Klauda, and W. Im
    CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems.
    J. Chem. Inf. Model. 53:2171-2180 (2013)
  1. X. Cheng, S. Jo, F.M. Marassi, and W. Im
    NMR-Based Simulation Studies of Pf1 Coat Protein in Explicit Membranes.
    Biophys. J. 105:691-698 (2013)
  1. Y. Qi and W. Im
    Quantification of Drive-Response Relationships Between Residues During Protein Folding.
    J. Chem. Theory Comput. 9:3799-3805 (2013)
  1. K.I. Lee, R.W. Pastor, O.S. Andersen, and W. Im
    Assessing Smectic Liquid-Crystal Continuum Models for Elastic Bilayer Deformations.
    Chem. Phys. Lipids 169:19-26 (2013)
  1. S. Jo, H.S. Lee, J. Skolnick, and W. Im
    Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling.
    PLoS Comput. Biol. 9:e1002946 (2013)
  1. S. Jo, W. Jiang, H.S. Lee, B. Roux, and W. Im
    CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application.
    J. Chem. Inf. Model. 53:267-277 (2013)
  1. S. Park and W. Im
    Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly.
    J. Chem. Theory Comput. 9:13-17 (2013)
  1. S. Jo and W. Im
    Glycan Fragment DB: A Database of PDB-based Glycan 3D Structures.   [www.glycanstructure.org]
    Nucleic Acids Res. 41:D470-D474 (2013)
  1. H. Rui, M. Rivera, and W. Im
    Protein Dynamics and Ion Traffic in Bacterioferritin.
    Biochemistry 51:9900-9910 (2012)
  1. H.S. Lee and W. Im
    Identification of Ligand Templates using Local Structure Alignment for Structure-based Drug Design.
    J. Chem. Inf. Model. 52:2784-2795 (2012)
  1. H.S. Lee, S. Jo, H-S. Lim, and W. Im
    Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors.
    J. Chem. Inf. Model. 52:1821-1832 (2012)
  1. J.B. Klauda, V. Monje, T. Kim, and W. Im
    Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains.
    J. Phys. Chem. B. 116:9424-9431 (2012)
  1. T. Kim, K.I. Lee, P. Morris, R.W. Pastor, O.S. Andersen, and W. Im
    Influence of Hydrophobic Mismatch on Structures and Dynamics of Gramicidin A and Lipid Bilayers.
    Biophys. J. 102:1551-1560 (2012)
  1. X. Cheng and W. Im
    NMR Observable-Based Structure Refinement of DAP12-NKG2C Activating Immunoreceptor Complex in Explicit Membranes.
    Biophys. J. 102:L27-L29 (2012)
  1. S. Park, T. Kim, and W. Im
    Transmembrane Helix Assembly with Window Exchange Umbrella Sampling.
    Phys. Rev. Lett. 108:108102 (2012)
  1. W. Im, S. Jo, and T. Kim
    An Ensemble Dynamics Approach to Decipher Solid-State NMR Observables of Membrane Proteins.
    Biochimica et Biophysica Acta (BBA) - Biomembranes 1818:252-262 (2012)
  1. K.I. Lee, S. Jo, H. Rui, B. Egwolf, B. Roux, R.W. Pastor, and W. Im
    Web Interface for Brownian Dynamics Simulation of Ion Transport and Its Applications to Beta-Barrel Pores.
    J. Comput. Chem. 33:331-339 (2012)  [cover]
  1. U. Golebiewska, J.G. Kay, T. Masters, S. Grinstein, W. Im, R.W. Pastor, S. Scarlata, and S. McLaughlin
    Evidence for a Fence/Corral that Impedes the Diffusion of Phosphatidylinositol 4,5-bisphosphate (PIP2) into and out of the Forming Phagosomes of Macrophages.
    Mol. Biol. Cell 22:3498-3507 (2011)
  1. S. Jo, K.C. Song, H. Desaire, A.D. MacKerell, Jr., and W. Im
    Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins.
    J. Comput. Chem. 32:3135-3141 (2011)  [cover]
  1. H. Rui, R. Kumar, and W. Im
    Membrane Tension, Lipid Adaptation, Conformational Changes, and Energetics in MscL Gating.
    Biophys. J. 101:671-679 (2011)
  1. H. Park, W. Im, and C. Seok
    Transmembrane Signaling of Chemotaxis Receptor Tar: Insights from Molecular Dynamics Simulation Studies.
    Biophys. J. 100:2955-2963 (2011)
  1. T. Kim, S. Jo, and W. Im
    Solid-State NMR Ensemble Dynamics as a Mediator Between Experiment and Simulation.
    Biophys. J. 100:2922-2928 (2011)
  1. S. Jo and W. Im
    Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables.
    Biophys. J. 100:2913-2921 (2011)
  1. K.C. Song, P.W. Livanec, J.B. Klauda, K. Kuczera, R.C. Dunn, and W. Im
    Orientation of Fluorescent Lipid Analog BODIPY-PC to Probe Lipid Membrane Properties: Insights from Molecular Dynamics Simulations.
    J. Phys. Chem. B. 115:6157–6165 (2011)
  1. K.I. Lee, H. Rui, R.W. Pastor, and W. Im
    Brownian Dynamics Simulations of Ion Transport through VDAC.
    Biophys. J. 100:611-619 (2011)
  1. H. Rui, K.I. Lee, R.W. Pastor, and W. Im
    Molecular Dynamics Studies of Ion Permeation in VDAC.
    Biophys. J. 100:602-610 (2011)
  1. J.H. Lee, Q. Zhang, S. Jo, S.C. Chai, M. Oh, W. Im, H. Lu, and H-S. Lim
    Novel Pyrrolopyrimidine-Based α-Helix Mimetics: Cell-Permeable Inhibitors of Protein-Protein Interactions.
    J. Am. Chem. Soc. 133:676-679 (2011)
  1. H. Rui and W. Im
    Protegrin-1 Orientation and Physicochemical Properties in Membrane Bilayers Studied by Potential of Mean Force Calculations.
    J. Comput. Chem. 31:2859-2867 (2010)
  1. S. Jo, H. Rui, J.B. Lim, J.B. Klauda, and W. Im
    Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies.
    J. Phys. Chem. B. 114:13342-13348 (2010)
  1. G. Jepkorir, J.C. Rodriguez, H. Rui, W. Im, S. Lovell, K.P. Battaile, A.Y. Alontaga, E. Yukl, P. Moenne-Loccoz, and M. Rivera
    Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa.
    J. Am. Chem. Soc. 132:9857–9872 (2010)
  1. T. Kim and W. Im
    Revisiting Hydrophobic Mismatch with Free Energy Simulation Studies of Transmembrane Helix Tilt and Rotation.
    Biophys. J. 99:175-183 (2010)
  1. K.H. Lim, P. Nagchowdhuri, T. Rathinavelan, and W. Im
    NMR Characterization of Hydrophobic Collapses in Amyloidogenic Partially Folded States and Their Implications for Protein Misfolding and Amyloid Formation.
    Biochem. Biophys. Res. Commun. 396:800-805 (2010)
  1. T. Rathinavelan, L. Zhang, W.L. Picking, D.D. Weis, R.N. De Guzman, and W. Im
    A Repulsive Electrostatic Mechanism for Protein Export through the Type III Secretion Apparatus.
    Biophys. J. 98:452-461 (2010)  [cover]
  1. H. Rui, J. Lee, and W. Im
    Comparative Molecular Dynamics Simulation Studies of Protegrin-1 Monomer and Dimer in Different Lipid Bilayers.
    Biophys. J. 97:787-795 (2009)
  1. S. Jo, J.B. Lim, J.B. Klauda, and W. Im
    CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes.
    Biophys. J. 97:50-58 (2009)
  1. W. Im, J. Lee, T. Kim, and H. Rui
    Novel Free Energy Calculations to Explore Mechanisms and Energetics of Membrane Protein Structure and Function.
    J. Comput. Chem. 30:1622-1633 (2009)
  1. B.R. Brooks, C.L. Brooks III, A.D. MacKerell, Jr., L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A.R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R.W. Pastor, C.B. Post, J.Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D.M. York, and M. Karplus
    CHARMM: The Biomolecular Simulation Program.
    J. Comput. Chem. 30:1545-1614 (2009)
  1. J. Lee, S. Ham, and W. 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. 30:1334-1343 (2009)
  1. T. Kim, J. Lee, and W. Im
    Molecular Dynamics Studies on Structure and Dynamics of Phospholamban Monomer and Pentamer in Membranes.
    Proteins 76:86-98 (2009)
  1. S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, and W. Im
    PBEQ-Solver for Online Visualization of Electrostatic Potential of Biomolecules.
    Nucleic Acids Res. 36:W270-W275 (2008)
  1. J. Lee, J. Chen, C.L. Brooks III, and W. Im
    Application of Solid-state NMR Restraint Potentials in Membrane Protein Modeling.
    J. Magn. Reson. 193:68-76 (2008)
  1. J. Lee and W. Im
    Role of Hydrogen Bonding and Helix-Lipid Interactions in Transmembrane Helix Association.
    J. Am. Chem. Soc. 130:6456-6462 (2008)
  1. S. Jo, T. Kim, V.G. Iyer, and W. Im
    CHARMM-GUI: A Web-based Graphical User Interface for CHARMM.
    J. Comput. Chem. 29:1859-1865 (2008)
  1. T. Rathinavelan and W. Im
    A Novel Strategy to Determine Protein Structures using Exclusively Residual Dipolar Coupling.
    J. Comput. Chem. 29:1640-1649 (2008)
  1. S.H. Park, C. Cheong, J. Idoyaga, J.Y. Kim, J-H Choi, Y. Do, H. Lee, J.H. Jo, Y-S Oh, W. Im, R.M. Steinman, and C.G. Park
    Generation and Application of New Rat Monoclonal Antibodies against Synthetic Tags for Improved Immunodetection.
    J. Immunol. Methods 331:27-38 (2008)
  1. J. Lee and W. Im
    Transmembrane Helix Tilting: Insights from Calculating the Potential of Mean Force.
    Phys. Rev. Lett. 100:018103 (2008)
  1. S. Jo, T. Kim, and W. Im
    Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations.
    PLoS ONE 2:e880 (2007)
  1. Y. Wang, A.N. Ouellette, C.W. Egan, T. Rathinavelan, W. Im and R.N. De Guzman
    Differences in the Electrostatic Surfaces of the Type III Secretion Needle Proteins.
    J. Mol. Biol. 371:1304-1314 (2007)
  1. J. Lee and W. Im
    Restrain Potential and Free Energy Decomposition for Helical Tilting.
    Chem. Phys. Lett. 441:132-135 (2007)
  1. T. Rathinavelan and W. Im
    Explicit Treatment of Force Contribution from Alignment Tensor using Overdetermined Linear Equations and Its Application in NMR Structure Determination.
    J. Comput. Chem. 28:1858-1864 (2007)
  1. J. Lee and W. Im
    Implementation and Application of Helix-Helix Distance and Crossing Angle Restraint Potentials.
    J. Comput. Chem. 28:669-680 (2007)
  1. L. Bu, W. Im, and C.L. Brooks III
    Membrane Assembly of Simple Helix Homo-oligomers Studied via Molecular Dynamics Simulations.
    Biophys. J. 92:854-863 (2007)
  1. Y. Liu, M. Scolari, W. Im, and H.J. Woo
    Protein-Protein Interactions in Actin-Myosin Binding and Structural Effects of R405Q Mutation: A Molecular Dynamics Study.
    Proteins 64:156-166 (2006)
  1. J. Chen, W. Im, and C.L. Brooks III
    Balancing Solvation and Intramolecular Interactions: Towards a Self-Consistent Generalized Born Force Field.
    J. Am. Chem. Soc. 128:3728-3736 (2006)
  1. W. Im, J. Chen, and C.L. Brooks III
    Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models.
    Adv. Protein Chem. 72: 173-198 (2006)
  1. J. Chen, W. Im, and C.L. Brooks III
    Application of Torsion Angle Molecular Dynamics for Efficient Sampling of Protein Conformation.
    J. Comput. Chem. 26: 1565-1578 (2005)
  1. W. Im and C.L. Brooks III
    Interfacial Folding and Membrane Insertion of Synthetic Peptides Studied by Molecular Dynamics Simulations.
    Proc. Natl. Acad. Sci. USA 102:6771-6776 (2005)
  1. J. Chen, H. Won, W. Im, H.J. Dyson and C.L. Brooks III
    Generation of Native-like Models from Limited NMR Data, Modern Force Fields and Advanced Conformational Sampling.
    J. Biomol. NMR 31:59-64 (2005)
  1. J. Chen, W. Im, and C.L. Brooks III
    Refinement of NMR Structure using Implicit Solvent and Advanced Sampling Techniques.
    J. Am. Chem. Soc. 126:16038-16047 (2004)
  1. S.Y. Noskov, W. Im, and B. Roux
    Ion Permeation through the α-Hemolysin Channel: Theoretical Studies based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory.
    Biophys. J. 87:2299-2309 (2004)
  1. B. Roux, T. Allen, S. Berneche, and W. Im
    Theoretical and Computational Models of Biological Ion Channels.
    Q. Rev. Biophys. 37:15-103 (2004)
  1. W. Im and C.L. Brooks III
    De Novo Folding of Membrane Proteins: An Exploration of the Structure and NMR Properties of the fd Coat Protein.
    J. Mol. Biol. 337:513-519 (2004)
  1. M. Feig, W. Im, and C.L. Brooks, III
    Implicit Solvation Based on Generalized Born Theory in Different Dielectric Environment.
    J. Chem. Phys. 120:903-911 (2004)
  1. M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case, and C.L. Brooks III
    Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures.
    J. Comput. Chem. 25:265-284 (2004)
  1. W. Im, M. Feig, and C.L. Brooks III
    An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins.
    Biophys. J. 85:2900-2918 (2003)
  1. W. Im, M.S. Lee, and C.L. Brooks III
    Generalized Born Model with a Simple Smoothing Function.
    J. Comput. Chem. 24:1691-1702 (2003)
  1. N.K. Banavali, W. Im, and B. Roux
    Electrostatic Free Energy Calculations using the Generalized Solvent Boundary Potential Method.
    J. Chem. Phys. 117:7381-7388 (2002)
  1. W. Im and B. Roux
    Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory.
    J. Mol. Biol. 322:851-869 (2002)
  1. W. Im and B. 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.
    J. Mol. Biol. 319:1177-1197 (2002)
  1. A. Philippsen, W. Im, A. Engel, T. Schirmer, B. Roux, and D.J. Muller
    Imaging the Electrostatic Potential of Transmembrane Channels: Atomic Probe Microscopy of OmpF Porin.
    Biophys. J. 82:1667-1676 (2002)
  1. W. Im and B. Roux
    Brownian Dynamics Simulations of Ions Channels: A General Treatment of the Electrostatic Reaction Field for Molecular Pores of Arbitrary Geometry.
    J. Chem. Phys. 115:4850-4861 (2001)
  1. W. Im, S. Berneche, and B. Roux
    Generalized Solvent Boundary Potentials for Computer Simulations.
    J. Chem. Phys. 114:2924-2937 (2001)
  1. B. Roux, S. Berneche and W. Im
    Ion Channels, Permeation, and Electrostatics: Insight into the Function of KcsA.
    Biochemistry 39:13295-13306 (2000)
  1. W. Im, S. Seefeld and B. Roux
    Grand Canonical Monte Carlo - Brownian Dynamics Algorithm for Simulating Ion Channels.
    Biophys. J. 79:788-801 (2000)
Before 2000
  1. M. Nina, W. Im, and B. Roux
    Optimized Atomic Radii for Protein Continuum Electrostatics Solvation Forces.
    Biophys. Chem. 78:89-96 (1999)
  1. W. Im, D. Beglov, and B. Roux
    Continuum Solvation Model: Computation of Electrostatic Forces from Numerical Solutions to the Poisson-Boltzmann Equation.
    Comput. Phys. Comm. 111:59-75 (1998)
  1. W. Im and Y. Won
    Molecular Dynamics Simulation on Thermodynamic and Structural Properties of Liquid Hydrocarbons: Normal Alkanes.
    bull. Korean Chem. Soc. 15:852-856 (1994)