REFEREED JOURNALS || BOOK CHAPTERS


2024

251. C.F. Roberts, Y. Cao, W. Im, R.A. Nichols, R.J. Lukas, and A.A. George
     Neuroprotective Amyloid-β N-terminal Peptides Differentially Alter Human α7- and α7β2-Nicotinic Acetylcholine Receptor Single-channel Properties.
     Br. J. Pharmacol. in press (2024)

250. J.R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M-K. Choi, D.S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E.B. Tadmor
     Type Label Framework for Bonded Force Fields in LAMMPS.
     J. Phys. Chem. B. in press (2024)

249. N.J. Wright, Y. Suo, F. Zhang, L. Kong, Y. Yin, J. Fedor, K. Sharma, M.J. Borgnia, W. Im, and S-Y. Lee
     Antiviral Drug Recognition and Elevator-type Transport Motions of CNT3.
     Nat. Chem. Biol. in press (2024)

248. S. Park, A. Rice, W. Im, and R. Pastor
     Spontaneous Curvature Generation by Peptides in Asymmetric Bilayers.
     J. Comput. Chem. 45:512-522 (2024)

247. T. Gopinath, K. Shin, Y. Tian, W. Im, J. Struppe, B. Perrone, A. Hassan, and F.M. Marassi
     Solid-state NMR MAS Cryoprobe Enables Structural Studies of Human Blood Protein Vitronectin Bound to Hydroxyapatite.
     J. Struct. Biol. 216:108061 (2024)

246. A.R. Hall, Y. Choi, W. Im, and D. Vavylonis
     Anillin-related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study.
     Structure 32:242-252.e2 (2024)

245. A.A. George, S.J. John, L.M. Lucero, J.B. Eaton, E. Jaiswal, Y. Cao, W. Im, J.M. McIntosh, P. Whiteaker
     Analogs of α-conotoxin PnIC Selectively Inhibit α7β2 Over α7-only Subtype Nicotinic Acetylcholine Receptors via a Novel Allosteric Mechanism.
     FASEB J. 38:e23374 (2024)

2023

244. T. Brown, M. Chavent, and W. Im
     Molecular Modelling and Simulation of Mycobacterial Cell Envelope: From Individual Components to Cell Envelope Assemblies.
     J. Phys. Chem. B. 127:10941-10949 (2023)

243. C. Choi, J. Bae, S. Kim, S. Lee, H. Kang, J. Kim, I. Bang, K.H. Kim, W-K. Huh, C. Seok, H. Park, W. Im, and H-J. Choi
     Understanding the Molecular Mechanisms of Odorant Binding and Activation of the Human OR52 Family.
     Nat. Commun. 14:8105 (2023)

242. W. Jiang, T. Wijerathne, H. Zhang, Y. Lin, S. Jo, W. Im, J.J. Lacroix, and Y.L. Luo
     Structural and Thermodynamic Framework for PIEZO1 Modulation by Small Molecules.
     Proc. Natl. Acad. Sci. USA 120:e2310933120 (2023)

241. K. Kanhaiya, M. Nathanson, P.J. in 't Veld, C. Zhu, I. Nikiforov, E.B. Tadmor, Y.K. Choi, W. Im, R.K. Mishra, and H. Heinz
     Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale.
     J. Chem. Theory Comput. 19:8293-8322 (2023)

240. L. Ghani, S. Kim, M. Ehsan, B. Lan, I.H. Poulsen, P. Hariharan, B. Byrne, L. Guan, C.J. Loland, X. Liu, W. Im, and P.S. Chae
     Melamine-cored Glucosides for Membrane Protein Solubilization and Stabilization: Importance of Water-mediated Intermolecular Hydrogen Bonding in Detergent Performance.
     Chem. Sci. 14:13014-1302 (2023)

239. J.A. Julien, A. Rousseau, T.V. Perone, D.M. LaGatta, C. Hong, K.T. Root, S. Park, R. Fuanta, W. Im, and K.J. Glover
     One-step Site-specific S-alkylation of Full-length Caveolin-1: Lipidation Modulates the Bilayer Depth of Its C-terminal Domain.
     Protein Sci. 32:e4791 (2023)

238. I.D. Pogozheva, S. Cherepanov, S-J. Park, M. Raghavan, W. Im, and A.L. Lomize
     Structural Modeling of Signaling Complexes of Homodimeric Cytokine Receptors with Natural Ligands and JAK2 Kinase using AlphaFold Multimer.
     J. Chem. Inf. Model. 63:5874-5895 (2023)

237. D. Hou, W. Cao, S. Kim, X. Cui, M. Ziarnik, W. Maury, W. Im, and X.F. Zhang
     Biophysical Properties of Interactions Between SARS-CoV-2 Spike Protein and Neuropilin-1.
     Protein Sci. 32:e4773 (2023)

236. S. Rizzo, E. Sikorski, S. Park, W. Im, V. Vasquez-Montes, A.S. Ladokhin, and D. Thévenin
     Promoting Protein Tyrosine Phosphatase J Activity with a pH-responsive Allosteric Transmembrane Agonist Inhibits Cancer-Associated Phenotypes.
     Protein Sci. 32:e4742 (2023)

235. H. Guterres and W. Im
     CHARMM-GUI-based Induced Fit Docking Workflow to Generate Reliable Ligand Binding Modes.
     J. Chem. Inf. Model. 63:4772-4779 (2023)

234. S. Park, I. Levental, R. Pastor, and W. Im
     Unsaturated Lipids Facilitate Partitioning of Transmembrane Peptides into Liquid Ordered Phases.
     J. Chem. Theory Comput. 19:5303-5314 (2023)

233. Y. Suo, N.J. Wright, H. Guterres, J.G. Fedor, K.J. Butay, M.J. Borgnia, W. Im, and S-Y. Lee
     Molecular Basis of Polyspecific Drug and Xenobiotic Recognition by OCT1 and OCT2.
     Nat. Struct. Mol. Biol. 30:1001-1011 (2023)

232. S-J. Park, N.R. Kern, T. Brown, J. Lee, and W. Im
     CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation.
     J. Mol. Biol. 435:167995 (2023)

231. D.H. Kwon, F. Zhang, B.A. McCray, S. Feng, M. Kumar, J.M. Sullivan, W. Im, C.J. Sumner, S-Y. Lee
     TRPV4-Rho GTPase Complex Structures Reveal Mechanisms of Gating and Disease.
     Nat. Commun. 14:3732 (2023)

230. J. Won, J. Kim, H. Jeong, J. Kim, S. Feng, B. Jeong, M. Kwak, J. Ko, W. Im, I. So, and H.H. Lee
     Molecular Architecture of Gαi-bound TRPC5 Ion Channel.
     Nat. Commun. 14:2550 (2023)

229. S. Feng, S. Park, Y.K. Choi, and W. Im
     CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications.
     J. Chem. Theory Comput. 19:2161-2185 (2023)

228. H. Kim, I-H. Jeong, Y.K. Choi, Y.K. Lee, E. Moon, Y. H. Huh, W. Im, J-O. Jin, M. Kwak, and P. C-W. Lee
     Suppression of Lung Cancer Malignancy by Micellized siRNA Through Cell Cycle Arrest.
     Adv. Healthc. Mater. 12:2202358 (2023)

227. Y. Gao, G. Widmalm, and W. Im
     Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides.
     J. Chem. Inf. Model. 63:1592-1601 (2023)

226. S.R. Lach, S. Kumar, S. Kim, W. Im, and A. Konovalova
     Conformational Rearrangements in the Sensory RcsF/OMP Complex Mediate Signal Transduction Across the Bacterial Cell Envelope.
     PLoS Genet. 19:e1010601 (2023)

225. C.M. Brown, R.A. Corey, A. Grélard, Y. Gao, Y.K. Choi, E. Luna, M. Gilleron, N. Destainville, A. Loquet, E. Fullam, W. Im, P.J. Stansfeld, M. Chavent
     Supramolecular Organisation and Dynamics of Mannosylated Phosphatidylinositol Lipids in the Mycobacterial Plasma Membrane.
     Proc. Natl. Acad. Sci. USA 120:e2212755120 (2023)

224. H. Kang, C. Park, Y.K. Choi, J. Bae, S. Kwon, J. Kim, C. Choi, C. Seok, W. Im, and H-J. Choi
     Structural Basis for Y2 Receptor-mediated Neuropeptide Y and Peptide YY Signaling.
     Structure 31:44-57 (2023)

223. S. Kim, Y. Liu, M. Ziarnik, S. Seo, Y. Cao, X.F. Zhang, and W. Im
     Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern.
     J. Comput. Chem. 44:594-601 (2023)

222. S. Feng, R.A. Pumroy, A.D. Protopopova, V.Y. Moiseenkova-Bell, and W. Im
     Modulation of TRPV2 by Endogenous and Exogenous Ligands: A Computational Study.
     Protein Sci. 32:e4490 (2023)

2022

221. H. Zhang, S. Kim, and W. Im
     Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations.
     J. Chem. Inf. Model. 62:6084-6093 (2022)

220. S. Ramesh, S. Park, W. Im, M.J. Call, and M.E. Call
     T-cell and B-cell Antigen Receptors Share a Conserved Core Transmembrane Structure.
     Proc. Natl. Acad. Sci. USA 119:e2208058119 (2022)

219. D. Suh, S. Feng, H. Lee, H. Zhang, S-J. Park, S. Kim, J. Lee, S. Choi, and W. Im
     CHARMM-GUI Enhanced Sampler for Various Collective Variables and Enhanced Sampling Methods.
     Protein Sci. 31:e4446 (2022)  [cover]

218. Y. Tian, K. Shin, A.E. Aleshin, W. Im, and F.M. Marassi
     Calcium-induced Environmental Adaptability of the Blood Protein Vitronectin.
     Biophys. J. 121:3896-3906 (2022)

217. Y. Yin, F. Zhang, S. Feng, K.J. Butay, M.J. Borgnia, W. Im, S-Y. Lee
     Activation Mechanism of the Mouse Cold-sensing TRPM8 Channel by Cooling Agonist and PIP2.
     Science 378:eadd1268 (2022)

216. K.W. Wang, J. Lee, H. Zhang, D. Suh, and W. Im
     CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs.
     J. Phys. Chem. B. 126:7354-7364 (2022)

215. N.J. Wright, J.G. Fedor, H. Zhang, P. Jeong, Y. Suo, J. Yoo, J. Hong, W. Im, S-Y. Lee
     Methotrexate Recognition by the Human Reduced Folate Carrier SLC19A1.
     Nature 609:1056-1062 (2022)

214. T. Das, X. Yang, H. Lee, E.H. Garst, E. Valencia, K. Chandran, W. Im, and H.C. Hang
     S-palmitoylation and Sterol Interactions Mediate Antiviral Specificity of IFITMs.
     ACS Chem. Biol. 17:2109-2120 (2022)

213. H. Guterres, S-J. Park, H. Zhang, T.V. Perone, J. Kim, and W. Im
     CHARMM-GUI High-Throughput Simulator for Efficient Evaluation of Protein-Ligand Interactions with Different Force Fields.
     Protein Sci. 31:e4413 (2022)

212. H-K. Choi, H. Kang, C. Lee, H.G. Kim, B.P. Phillips, S. Park, C. Tumescheit, S.A. Kim, H. Lee, S-H. Roh, H. Hong, M. Steinegger, W. Im, E.A. Miller, H-J. Choi, and T-Y. Yoon
     Evolutionary Balance Between Foldability and Functionality of a Glucose Transporter.
     Nat. Chem. Biol. 18:713-723 (2022)

211. J. Rizo, L. Sari, Y. Qi, W. Im, and M.M. Lin
     All-atom Molecular Dynamics Simulations of Synaptotagmin-SNARE-Complexin Complexes Bridging a Vesicle and a Flat Lipid Bilayer.
     eLife 11:e76356 (2022)

210. S. Feng, L. Kong, S. Gee, and W. Im
     Molecular Condensate in a Membrane: A Tugging Game Between Hydrophobicity and Polarity with Its Biological Significance.
     Langmuir 19:5955-5962 (2022)

209. L. Ghani, S. Kim, H. Wang, H.S. Lee, J.S. Mortensen, S. Katsube, Y. Du, A. Sadaf, W Ahmed, B. Byrne, L. Guan, C.J. Loland, B.K. Kobilka, W. Im, and P.S. Chae
     Foldable Detergents for Membrane Protein Study: Importance of Detergent Core Flexibility in Protein Stabilization.
     Chem. Eur. J. 28:e2022001 (2022)

208. I.D. Pogozheva, G.A. Armstrong, L. Kong, T.J. Hartnagel, C.A. Carpino, S.E. Gee, D.M. Picarello, A.S. Rubin, J. Lee, S. Park, A.L. Lomize, and W. Im
     Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes.
     J. Chem. Inf. Model. 62:1036-1051 (2022)

207. C. Park, J. Kim, S-B. Ko, Y.K. Choi, H. Jeong, H. Woo, H. Kang, I. Bang, S.A. Kim, T-Y. Yoon, C. Seok, W. Im, and H-J. Choi
     Structural Basis of Neuropeptide Y Signaling Through Y1 Receptor.
     Nat. Commun. 13:853 (2022)

206. Y.K. Choi, N.R. Kern, S. Kim, K. Kanhaiya, S.H. Jeon, Y. Afshar, S. Jo, B.R. Brooks, J. Lee, E.B. Tadmor, H. Heinz, and W. Im
     CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.
     J. Chem. Theory Comput. 18:479-493 (2022)

205. A. Kognole, J. Lee, S-J. Park, S. Jo, P. Chatterjee, J. Lemkul, J. Huang, A.D. MacKerell, Jr., and W. Im
     CHARMM-GUI Drude Prepper for Molecular Dynamics Simulation Using the Classical Drude Polarizable Force Field.
     J. Comput. Chem. 43:359-375 (2022)

2021

204. S. Kim, Y. Liu, Z. Lei, J. Dicker, Y. Cao, X.F. Zhang, and W. Im
     Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern.
     J. Chem. Theory Comput. 17:7972-7979 (2021)

203. A. Pisapati, W. Cao, K.R. Anderson, G. Jones, K. Hoffman, P. Whiteaker, W. Im, X.F. Zhang, and J.M. Miwa
     Biophysical Characterization of Lynx-Nicotinic Receptor Interactions Using Atomic Force Microscopy.
     FASEB Bioadv. 3:1034-1042 (2021)

202. H. Guterres, S-J. Park, Y. Cao, and W. Im
     CHARMM-GUI Ligand Designer for Template-based Ab Initio Ligand Design in a Binding Site.
     J. Chem. Inf. Model. 61:5336-5342 (2021)

201. N. Ferraro, S. Kim, W. Im, and M.M. Pires
     Systematic Assessment of Accessibility to the Surface of Staphylococcus aureus.
     ACS Chem. Biol. 16:2527-2536 (2021)

200. S. Park, W. Im, and R.W. Pastor
     Developing Initial Conditions for Simulations of Asymmetric Membranes: A Practical Recommendation.
     Biophys. J. 120:5041-5059 (2021)

199. S. Park, Y.K. Choi, S. Kim, J. Lee, and W. Im
     CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids.
     J. Chem. Inf. Model. 61:5192-5202 (2021)

198. Y. Cao, Y.K. Choi, M. Frank, H. Woo, S.-J. Park, M.S. Yeom, C. Seok, and W. Im
     Dynamic Interactions of Fully-glycosylated SARS-CoV-2 Spike Protein with Various Antibodies.
     J. Chem. Theory Comput. 17:6559-6569 (2021)

197. H. Zhang, S. Kim , T.J. Giese, T-S. Lee, J. Lee, D.M. York, and W. Im
     CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER.
     J. Chem. Inf. Model. 61:4145-4151 (2021)

196. A.E. Aleshin, Y. Yao, A. Iftikhar, A.A. Bobkov, J. Yu, G. Cadwell, M.G. Klein, C. Dong, L.A. Bankston, R.C. Liddington, W. Im, G. Powis, FM. Marassi
     Structural Basis for the Association of PLEKHA7 with Membrane-embedded Phosphatidylinositol Lipids.
     Structure 29:1029-1039 (2021)

195. H. Guterres, S-J. Park, H. Zhang, and W. Im
     CHARMM-GUI LBS Finder and Refiner for Ligand-Binding-Site Prediction and Refinement.
     J. Chem. Inf. Model. 61:3744-3751 (2021)

194. S. Aiman, S. Kim, H.E. Bae, H. Wang, A. Nygaard, Y. Uegaki, Y. Du, C.F. Munk, S. Katsube, J. Bae, C.W. Choi, H-J. Choi, B. Byrne, S.H. Gellman, L. Guan, C.J. Loland, B.K. Kobilka, W. Im, and P.S. Chae
     Conformationally Flexible Core-bearing Detergents with a Hydrophobic or Hydrophilic Pendant: Effect of Pendant Polarity on Detergent Conformation and Membrane Protein Stability.
     Acta Biomater. 128:393-407 (2021)

193. A. Croitoru, S-J. Park, A. Kumar, J. Lee, W. Im, A.D. MacKerell, Jr., and A. Aleksandrov
     Additive CHARMM36 Force Field for Nonstandard Amino Acids.
     J. Chem. Theory Comput. 17:3554-3570 (2021)

192. C. Dong, Y.K. Choi, J. Lee, X.F. Zhang, A Honerkamp-Smith, G. Widmalm, L.J. Lowe-Krentz, and W. im
     Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane.
     Glycobiology 31:593-602 (2021)  [cover]

191. E. Garst, H. Lee, T. Das, S. Bhattacharya, A. Percher, R. Wiewiora, I. Witte, Y. Li, T. Peng, W. Im, and H.C. Hang
     Site-specific Lipidation Enhances IFITM3 Membrane Interactions and Antiviral Activity.
     ACS Chem. Biol. 16:844-856 (2021)

190. S. Feng, R. Wang, R.W. Pastor, J.B. Klauda, and W. Im
     Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein-Lipid Modulations in Archaeal Membranes.
     J. Phys. Chem. B. 125:4714-4725 (2021)

189. C. Zhou, H. Shi, M. Zhang, L. Zhou, L. Xiao, S. Feng, W. Im, M. Zhou, X. Zhang, and Y. Huang
     Structural Insight into Phospholipid Transport by the MlaFEBD Complex from P. aeruginosa.
     J. Mol. Biol. 433:166986 (2021)

188. Y.K. Choi, S-J. Park, S. Park, S. Kim, N.R. Kern, J. Lee, and W. Im
     CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers.
     J. Chem. Theory Comput. 17:2431-2443 (2021)

187. Y.K. Choi, Y. Cao, M. Frank, H. Woo, S.-J. Park, M.S. Yeom, T.I. Croll, C. Seok, and W. Im
     Structure, Dynamics, Receptor Binding, and Antibody Binding of Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane.
     J. Chem. Theory Comput. 17:2479-2487 (2021)  [cover]

186. W. Cao, C. Dong, S. Kim, D. Hou, W. Tai, L. Du, W. Im, and X.F. Zhang
     Biomechanical Characterization of SARS-CoV-2 Spike RBD and human ACE2 Protein-Protein Interaction.   [News Article]
     Biophys. J. 120:1011-1019 (2021)

185. E. Luna, S. Kim, Y. Gao, G. Widmalm, and W. Im
     Influences of Vibrio cholerae Lipid A Types on LPS Bilayer Properties.
     J. Phys. Chem. B. 125:2105-2112 (2021)

184. Y. Gao, J. Lee, I.P.S. Smith, H. Lee, S. Kim, Y. Qi, J.B. Klauda, G. Widmalm, S. Khalid, and W. Im
     CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides.
     J. Chem. Inf. Model. 61:831-839 (2021)

183. Y. Cao, S-J. Park, and W. Im
     A Systematic Analysis of Protein-Carbohydrate Interactions in the Protein Data Bank.
     Glycobiology 31:126-136 (2021)

182. K. Kanhaiya, S. Kim, W. Im, and H. Heinz
     Accurate Simulation of Surfaces and Interfaces of Ten FCC Metals and Steel Using Lennard-Jones Potentials.
     Npj Comput. Mater 7:17 (2021)

181. H. Guterres, S-J. Park, W. Jiang, and W. Im
     Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.
     J. Chem. Inf. Model. 61:535-546 (2021)

2020

180. S. Ramesh, S. Park, M.J Call, W. Im and M.E. Call
     Experimentally Guided Computational Methods Yield Highly Accurate Insights into Transmembrane Interactions within the T Cell Receptor Complex.
     J. Phys. Chem. B. 124:10303-10310 (2020)

179. S. Kim, H. Oshima, H. Zhang, N.R. Kern, S. Re, J. Lee, B. Roux, Y. Sugita, W. Jiang, and W. Im
     CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations.
     J. Chem. Theory Comput. 16:7207-7218 (2020)

178. K. Shin, J.E. Kent, C. Singh, L.M. Fujimoto, Y. Tian, W. Im, and F.M. Marassi
     Calcium and Hydroxyapatite Binding Properties of Human Vitronectin Provide New Insights for Abnormal Deposit Formation.
     Proc. Natl. Acad. Sci. USA 117:18504-18510 (2020)

177. P. Ryzhov, Y. Tian, Y. Yao, A.A. Bobkov, W. Im, and F.M. Marassi
     Conformational States of the Cytoprotective Protein Bcl-xL.
     Biophys. J. 119:1324-1334 (2020)  [cover]

176. J. Lee, M. Hitzenberger, M. Rieger, N.R. Kern, M. Zacharias, and W. Im
     CHARMM-GUI Supports the Amber Force Fields.
     J. Chem. Phys. 153:035103 (2020)

175. H. Woo, S-J. Park, Y.K. Choi, T. Park, M. Tanveer, Y. Cao, N.R. Kern, J. Lee, M.S. Yeom, T.I. Croll, C. Seok, and W. Im
     Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane.   [News Article]
     J. Phys. Chem. B. 124:7128-7137 (2020)  [cover]

174. Y. Gao, J. Lee, G. Widmalm, and W. Im
     Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen.
     J. Phys. Chem. B. 124:5948-5956 (2020)

173. C. Singh, H. Lee, Y. Tian, S.S. Bartra, S. Hower, L.M. Fujimoto, Y. Yao, S.A. Ivanov, R.Z. Shaikhutdinova, A.P. Asinimov, G.V. Plano, W. Im, and F.M. Marassi
     Mutually Constructive Roles of Ail and LPS in Yersinia pestis Serum Survival.
     Mol. Microbiol. 14:510-520 (2020)  [cover]

172. A. Suppahia, P. Itagi, A. Burris, F.M.G.Kim, A. Vontz, A. Kante, S. Kim, W. Im, E. Deeds, J. Roelofs
     Cooperativity in Proteasome Core Particle Maturation.
     iScience 23:101090 (2020)

171. D.S. Patel, P. Morales, G. Widmalm, and W. Im
     Escherichia coli O176 LPS Structure and Dynamics: A NMR Spectroscopy and MD Simulation Study
     Curr. Res. Struct. Biol. 2:79-88 (2020)

170. G. Ongwae, K. Morrison, R. Allen, S. Kim, W. Im, W. Wuest, and M. Pires
     Broadening Activity of Polymyxin by Quaternary Ammonium Grafting.
     ACS Infect. Dis. 6:1427-1435 (2020)

169. C. Dong, N.R. Kern, 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.
     J. Phys. Chem. B. 124:4017-4025 (2020)  [cover]

168. H. Guterres and W. Im
     Improvement of Protein-Ligand Docking Results Using High-Throughput Molecular Dynamics Simulations.
     J. Chem. Inf. Model. 60:2189-2198 (2020)

167. Y. Cao, S-J. Park, A.Y. Mehta, R.D. Cummings, and W. Im
     GlyMDB: Glycan Microarray Database and Analysis Toolset.
     Bioinformatics 36:2438-2442 (2020)

166. W. Im and S. Khalid
     Molecular Simulations of Bacterial Membranes Come of Age.
     Annu. Rev. Phys. Chem. 71:8.1-8.18 (2020)

165. Y. Gao, J. Lee, G. Widmalm, and W. Im
     Preferred Conformations of Lipooligosaccharides and Oligosaccharides of Moraxella catarrhalis.
     Glycobiology 30:86-94 (2020)

164. 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. 41:415-420 (2020)

2019

163. 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 116:24562-24567 (2019)

162. 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. 15:6491-6503 (2019)

161. 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. 15:6524-6535 (2019)

160. 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)

159. 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)

158. H.S. Lee and W. Im
     Stalis: A Computational Method for Template-based Ab Initio Ligand Design.
     J. Comput. Chem. 40:1622-1632 (2019)

157. 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)

156. 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)

155. 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)

154. 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)

153. 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)

152. 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]

2018

151. S. Kim, M.M. Pires, and W. Im
     Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes.
     Sci. Rep. 8:17704 (2018)

150. 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)

149. 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)

148. 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)

147. 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)

146. 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)

145. 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)

144. S. Park and W. Im
     Quantitative Characterization of Cholesterol Partitioning Between Binary Bilayers.
     J. Chem. Theory Comput. 14:2829-2833 (2018)

143. 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)

142. 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)

141. 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]

140. 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)

2017

139. 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)

138. 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)

137. 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)

136. 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 LF_N Bound PA Pore.
     Toxins 9:298 (2017)

135. 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]

134. 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]

133. 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)

132. 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)

131. 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)

130. 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)

129. 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)

128. 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)

127. 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)

126. 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)

125. 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)

124. 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)

123. 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)

2016

122. 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)

121. 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)

120. 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)

119. 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)

118. 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)

117. 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)

116. 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)

115. 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)

114. 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)

113. 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)

112. 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)

111. 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)

110. 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)

109. 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)

108. Y. Qi, S. Jo, and W. Im
     Roles of Glycans in Interactions Between gp120 and HIV Broadly Neutralizing Antibodies.
     Glycobiology 26:251-260 (2016)

107. 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)

106. 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)

105. 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)

104. S. Jo, Y. Qi, and W. Im
     Preferred Conformations of N-glycan Core Pentasaccharide in Solution and in Glycoproteins.
     Glycobiology 26:19-29 (2016)

2015

103. 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)

102. 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)

101. 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)

100. S. Park, A.H. Beaven, J.B. Klauda, and W. Im
     How Tolerant are Membrane Simulations with Mismatch in Area per Lipid Between Leaflets?
     J. Chem. Theory Comput. 11:3466-3477 (2015)

99. 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)

98. 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)

97. 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)

96. 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)

95. 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)

94. 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)

2014

93. 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)

92. 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)

91. 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)

90. 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)

89. 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]

88. 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)

87. 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)

86. S. Park and W. Im
    Theory of Adaptive Optimization for Umbrella Sampling.
    J. Chem. Theory Comput. 10:2719-2728 (2014)

85. 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]

84. 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)

83. 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]

82. 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)

81. 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)

80. 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)

2013

79. 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)

78. 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)

77. 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)

76. 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)

75. Y. Qi and W. Im
    Quantification of Drive-Response Relationships Between Residues During Protein Folding.
    J. Chem. Theory Comput. 9:3799-3805 (2013)

74. 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)

73. 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)

72. 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)

71. S. Park and W. Im
    Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly.
    J. Chem. Theory Comput. 9:13-17 (2013)

70. 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)

2012

69. H. Rui, M. Rivera, and W. Im
    Protein Dynamics and Ion Traffic in Bacterioferritin.
    Biochemistry 51:9900-9910 (2012)

68. 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)

67. 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)

66. 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)

65. 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)

64. 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)

63. S. Park, T. Kim, and W. Im
    Transmembrane Helix Assembly with Window Exchange Umbrella Sampling.
    Phys. Rev. Lett. 108:108102 (2012)

62. 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)

61. 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]

2011

60. 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)

59. 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]

58. H. Rui, R. Kumar, and W. Im
    Membrane Tension, Lipid Adaptation, Conformational Changes, and Energetics in MscL Gating.
    Biophys. J. 101:671-679 (2011)

57. 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)

56. 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)

55. 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)

54. 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)

53. 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)

52. 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)

51. 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)

2010

50. 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)

49. 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)

48. 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)

47. 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)

46. 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)

45. 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]

2009

44. 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)

43. 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)

42. 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)

41. 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)

40. 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)

39. 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)

2008

38. 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)

37. 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)

36. 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)

35. 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)

34. T. Rathinavelan and W. Im
    A Novel Strategy to Determine Protein Structures Using Exclusively Residual Dipolar Coupling.
    J. Comput. Chem. 29:1640-1649 (2008)

33. 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)

32. J. Lee and W. Im
    Transmembrane Helix Tilting: Insights from Calculating the Potential of Mean Force.
    Phys. Rev. Lett. 100:018103 (2008)

2007

31. S. Jo, T. Kim, and W. Im
    Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations.
    PLoS ONE 2:e880 (2007)

30. 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)

29. J. Lee and W. Im
    Restrain Potential and Free Energy Decomposition for Helical Tilting.
    Chem. Phys. Lett. 441:132-135 (2007)

28. 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)

27. J. Lee and W. Im
    Implementation and Application of Helix-Helix Distance and Crossing Angle Restraint Potentials.
    J. Comput. Chem. 28:669-680 (2007)

26. 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)

2006

25. 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)

24. 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)

23. 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)

2005

22. 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)

21. 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)

20. 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)

2004

19. 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)

18. 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)

17. B. Roux, T. Allen, S. Berneche, and W. Im
    Theoretical and Computational Models of Biological Ion Channels.
    Q. Rev. Biophys. 37:15-103 (2004)

16. 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)

15. 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)

14. 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)

2003

13. 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)

12. 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)

2002

11. 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)

10. 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)

9. 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)

8. 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)

2001

7. 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)

6. W. Im, S. Berneche, and B. Roux
   Generalized Solvent Boundary Potentials for Computer Simulations.
   J. Chem. Phys. 114:2924-2937 (2001)

2000

5. B. Roux, S. Berneche and W. Im
   Ion Channels, Permeation, and Electrostatics: Insight into the Function of KcsA.
   Biochemistry 39:13295-13306 (2000)

4. 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

3. M. Nina, W. Im, and B. Roux
   Optimized Atomic Radii for Protein Continuum Electrostatics Solvation Forces.
   Biophys. Chem. 78:89-96 (1999)

2. 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)