| Year |
Citation |
Score |
| 2023 |
Hall AR, Choi YK, Im W, Vavylonis D. Anillin-related Mid1 as an adaptive and multimodal contractile ring anchoring protein: A simulation study. Structure (London, England : 1993). PMID 38103546 DOI: 10.1016/j.str.2023.11.010 |
0.319 |
|
| 2023 |
Jiang W, Wijerathne TD, Zhang H, Lin YC, Jo S, Im W, Lacroix JJ, Luo YL. Structural and thermodynamic framework for PIEZO1 modulation by small molecules. Proceedings of the National Academy of Sciences of the United States of America. 120: e2310933120. PMID 38060566 DOI: 10.1073/pnas.2310933120 |
0.648 |
|
| 2023 |
Ghani L, Kim S, Ehsan M, Lan B, Poulsen IH, Dev C, Katsube S, Byrne B, Guan L, Loland CJ, Liu X, Im W, Chae PS. Melamine-cored glucosides for membrane protein solubilization and stabilization: importance of water-mediated intermolecular hydrogen bonding in detergent performance. Chemical Science. 14: 13014-13024. PMID 38023530 DOI: 10.1039/d3sc03543c |
0.335 |
|
| 2023 |
Kern NR, Lee J, Choi YK, Im W. CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems. Biorxiv : the Preprint Server For Biology. PMID 37693396 DOI: 10.1101/2023.08.30.555590 |
0.306 |
|
| 2023 |
Park SJ, Kern N, Brown T, Lee J, Im W. CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation. Journal of Molecular Biology. 435: 167995. PMID 37356910 DOI: 10.1016/j.jmb.2023.167995 |
0.328 |
|
| 2023 |
Feng S, Park S, Choi YK, Im W. CHARMM-GUI : Past, Current, and Future Developments and Applications. Journal of Chemical Theory and Computation. PMID 37014931 DOI: 10.1021/acs.jctc.2c01246 |
0.368 |
|
| 2023 |
Hall AR, Choi YK, Im W, Vavylonis D. Anillin Related Mid1 as an Adaptive and Multimodal Contractile Ring Anchoring Protein: A Simulation Study. Biorxiv : the Preprint Server For Biology. PMID 36747616 DOI: 10.1101/2023.01.27.525865 |
0.31 |
|
| 2023 |
Brown CM, Corey RA, Grélard A, Gao Y, Choi YK, Luna E, Gilleron M, Destainville N, Nigou J, Loquet A, Fullam E, Im W, Stansfeld PJ, Chavent M. Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane. Proceedings of the National Academy of Sciences of the United States of America. 120: e2212755120. PMID 36693100 DOI: 10.1073/pnas.2212755120 |
0.32 |
|
| 2022 |
Feng S, Pumroy RA, Protopopova AD, Moiseenkova-Bell VY, Im W. Modulation of TRPV2 by Endogenous and Exogenous Ligands: A Computational Study. Protein Science : a Publication of the Protein Society. e4490. PMID 36327382 DOI: 10.1002/pro.4490 |
0.376 |
|
| 2022 |
Wang KW, Lee J, Zhang H, Suh D, Im W. CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs. The Journal of Physical Chemistry. B. 126: 7354-7364. PMID 36117287 DOI: 10.1021/acs.jpcb.2c05294 |
0.312 |
|
| 2022 |
Rizo J, Sari L, Qi Y, Im W, Lin MM. All-atom molecular dynamics simulations of Synaptotagmin-SNARE-complexin complexes bridging a vesicle and a flat lipid bilayer. Elife. 11. PMID 35708237 DOI: 10.7554/eLife.76356 |
0.336 |
|
| 2022 |
Feng S, Kong L, Gee S, Im W. Molecular Condensate in a Membrane: A Tugging Game between Hydrophobicity and Polarity with Its Biological Significance. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 35503859 DOI: 10.1021/acs.langmuir.2c00876 |
0.36 |
|
| 2022 |
Choi HK, Kang H, Lee C, Kim HG, Phillips BP, Park S, Tumescheit C, Kim SA, Lee H, Roh SH, Hong H, Steinegger M, Im W, Miller EA, Choi HJ, et al. Evolutionary balance between foldability and functionality of a glucose transporter. Nature Chemical Biology. PMID 35484435 DOI: 10.1038/s41589-022-01002-w |
0.315 |
|
| 2022 |
Pogozheva ID, Armstrong GA, Kong L, Hartnagel TJ, Carpino CA, Gee SE, Picarello DM, Rubin AS, Lee J, Park S, Lomize AL, Im W. Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes. Journal of Chemical Information and Modeling. PMID 35167752 DOI: 10.1021/acs.jcim.1c01514 |
0.374 |
|
| 2021 |
Kognole AA, Lee J, Park SJ, Jo S, Chatterjee P, Lemkul JA, Huang J, MacKerell AD, Im W. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. Journal of Computational Chemistry. PMID 34874077 DOI: 10.1002/jcc.26795 |
0.632 |
|
| 2021 |
Choi YK, Kern NR, Kim S, Kanhaiya K, Afshar Y, Jeon SH, Jo S, Brooks BR, Lee J, Tadmor EB, Heinz H, Im W. CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems. Journal of Chemical Theory and Computation. PMID 34871001 DOI: 10.1021/acs.jctc.1c00996 |
0.599 |
|
| 2021 |
Park S, Choi YK, Kim S, Lee J, Im W. CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids. Journal of Chemical Information and Modeling. PMID 34546048 DOI: 10.1021/acs.jcim.1c00770 |
0.337 |
|
| 2021 |
Gao Y, Lee J, Widmalm G, Im W. Correction to "Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen". The Journal of Physical Chemistry. B. PMID 34351153 DOI: 10.1021/acs.jpcb.1c06516 |
0.318 |
|
| 2021 |
Park S, Choi YK, Kim S, Lee J, Im W. CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids. Biorxiv : the Preprint Server For Biology. PMID 34189527 DOI: 10.1101/2021.06.23.449544 |
0.34 |
|
| 2021 |
Sadaf A, Kim S, Bae HE, Wang H, Nygaard A, Uegaki Y, Du Y, Munk CF, Katsube S, Bae J, Choi CW, Choi HJ, Byrne B, Gellman SH, Guan L, ... ... Im W, et al. Conformationally flexible core-bearing detergents with a hydrophobic or hydrophilic pendant: Effect of pendant polarity on detergent conformation and membrane protein stability. Acta Biomaterialia. PMID 33933694 DOI: 10.1016/j.actbio.2021.04.043 |
0.301 |
|
| 2021 |
Feng S, Wang R, Pastor RW, Klauda JB, Im W. Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein-Lipid Modulations in Archaeal Membranes. The Journal of Physical Chemistry. B. PMID 33913729 DOI: 10.1021/acs.jpcb.1c01930 |
0.377 |
|
| 2021 |
Aleshin AE, Yao Y, Iftikhar A, Bobkov AA, Yu J, Cadwell G, Klein MG, Dong C, Bankston LA, Liddington RC, Im W, Powis G, Marassi FM. Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids. Structure (London, England : 1993). PMID 33878292 DOI: 10.1016/j.str.2021.03.018 |
0.306 |
|
| 2021 |
Choi YK, Cao Y, Frank M, Woo H, Park SJ, Yeom MS, Croll TI, Seok C, Im W. Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane. Journal of Chemical Theory and Computation. PMID 33689337 DOI: 10.1021/acs.jctc.0c01144 |
0.317 |
|
| 2021 |
Luna E, Kim S, Gao Y, Widmalm G, Im W. Influences of Lipid A Types on LPS Bilayer Properties. The Journal of Physical Chemistry. B. PMID 33600188 DOI: 10.1021/acs.jpcb.0c09144 |
0.34 |
|
| 2021 |
Gao Y, Lee J, Smith IPS, Lee H, Kim S, Qi Y, Klauda JB, Widmalm G, Khalid S, Im W. CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. Journal of Chemical Information and Modeling. PMID 33442985 DOI: 10.1021/acs.jcim.0c01360 |
0.302 |
|
| 2020 |
Kim S, Oshima H, Zhang H, Kern NR, Re S, Lee J, Roux B, Sugita Y, Jiang W, Im W. CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations. Journal of Chemical Theory and Computation. PMID 33112150 DOI: 10.1021/acs.jctc.0c00884 |
0.458 |
|
| 2020 |
Dong C, Choi YK, Lee J, Zhang XF, Honerkamp-Smith A, Widmalm G, Lowe-Krentz LJ, Im W. Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane. Glycobiology. PMID 33021626 DOI: 10.1093/glycob/cwaa092 |
0.387 |
|
| 2020 |
Ryzhov P, Tian Y, Yao Y, Bobkov AA, Im W, Marassi FM. Conformational States of the Cytoprotective Protein Bcl-xL. Biophysical Journal. PMID 32888404 DOI: 10.1016/J.Bpj.2020.08.014 |
0.458 |
|
| 2020 |
Lee J, Hitzenberger M, Rieger M, Kern NR, Zacharias M, Im W. CHARMM-GUI supports the Amber force fields. The Journal of Chemical Physics. 153: 035103. PMID 32716185 DOI: 10.1063/5.0012280 |
0.371 |
|
| 2020 |
Cao Y, Park SJ, Im W. A Systematic Analysis of Protein-Carbohydrate Interactions in the PDB. Glycobiology. PMID 32614943 DOI: 10.1093/Glycob/Cwaa062 |
0.356 |
|
| 2020 |
Woo H, Park SJ, Choi YK, Park T, Tanveer M, Cao Y, Kern NR, Lee J, Yeom MS, Croll TI, Seok C, Im W. Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane. The Journal of Physical Chemistry. B. PMID 32559081 DOI: 10.1021/Acs.Jpcb.0C04553 |
0.45 |
|
| 2020 |
Woo H, Park SJ, Choi YK, Park T, Tanveer M, Cao Y, Kern NR, Lee J, Yeom MS, Croll T, Seok C, Im W. Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane. Biorxiv : the Preprint Server For Biology. PMID 32511389 DOI: 10.1101/2020.05.20.103325 |
0.351 |
|
| 2020 |
Gao Y, Lee J, Widmalm G, Im W. Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigens. The Journal of Physical Chemistry. B. PMID 32476421 DOI: 10.1021/Acs.Jpcb.0C03353 |
0.409 |
|
| 2020 |
Singh C, Lee H, Tian Y, Schesser Bartra S, Hower S, Fujimoto LM, Yao Y, Ivanov SA, Shaikhutdinova RZ, Anisimov AP, Plano GV, Im W, Marassi FM. Mutually constructive roles of Ail and LPS in Yersinia pestis serum survival. Molecular Microbiology. PMID 32462782 DOI: 10.1111/Mmi.14530 |
0.322 |
|
| 2020 |
Guterres H, Im W. Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. PMID 32227880 DOI: 10.1021/Acs.Jcim.0C00057 |
0.38 |
|
| 2020 |
Ongwae G, Morrison KR, Allen RA, Kim S, Im W, Wuest W, Pires MM. Broadening Activity of Polymyxin by Quaternary Ammonium Grafting. Acs Infectious Diseases. PMID 32212668 DOI: 10.1021/Acsinfecdis.0C00037 |
0.323 |
|
| 2020 |
Dong C, Kern NR, Anderson KR, Zhang XF, Miwa JM, Im W. Dynamics and Interactions of GPI-Linked Lynx1 Protein with/without Nicotinic Acetylcholine Receptor in Membrane Bilayers. The Journal of Physical Chemistry. B. PMID 32208709 DOI: 10.1021/Acs.Jpcb.0C00159 |
0.367 |
|
| 2020 |
Im W, Khalid S. Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age. Annual Review of Physical Chemistry. PMID 32070216 DOI: 10.1146/Annurev-Physchem-103019-033434 |
0.452 |
|
| 2020 |
Im W, Banavali N, Luo YL. Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane. Journal of Computational Chemistry. 41: 385-386. PMID 31943239 DOI: 10.1002/Jcc.26140 |
0.477 |
|
| 2019 |
Cao Y, Park SJ, Mehta AY, Cummings RD, Im W. GlyMDB: Glycan Microarray Database and Analysis Toolset. Bioinformatics (Oxford, England). PMID 31841142 DOI: 10.1093/Bioinformatics/Btz934 |
0.345 |
|
| 2019 |
Nawrocki G, Im W, Sugita Y, Feig M. Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending. Proceedings of the National Academy of Sciences of the United States of America. PMID 31740611 DOI: 10.1073/Pnas.1910771116 |
0.465 |
|
| 2019 |
Gao Y, Lee J, Widmalm G, Im W. Preferred Conformations of Lipooligosaccharides and Oligosaccharides of Moraxella catarrhalis. Glycobiology. PMID 31616921 DOI: 10.1093/Glycob/Cwz086 |
0.375 |
|
| 2019 |
Dong C, Kania S, Morabito M, Zhang XF, Im W, Oztekin A, Cheng X, Webb EB. A mechano-reactive coarse-grained model of the blood-clotting agent von Willebrand factor. The Journal of Chemical Physics. 151: 124905. PMID 31575216 DOI: 10.1063/1.5117154 |
0.322 |
|
| 2019 |
Park S, Yeom MS, Andersen OS, Pastor RW, Im W. Quantitative Characterization of Protein-Lipid Interactions by Free Energy Simulation Between Binary Bilayers. Journal of Chemical Theory and Computation. PMID 31560853 DOI: 10.1021/Acs.Jctc.9B00815 |
0.462 |
|
| 2019 |
Guterres H, Lee HS, Im W. Ligand-Binding Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates. Journal of Chemical Theory and Computation. PMID 31557013 DOI: 10.1021/Acs.Jctc.9B00751 |
0.345 |
|
| 2019 |
Qi Y, Lee J, Cheng X, Shen R, Islam SM, Roux B, Im W. CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations. Journal of Computational Chemistry. PMID 31329318 DOI: 10.1002/Jcc.26032 |
0.531 |
|
| 2019 |
Kesireddy A, Pothula KR, Lee J, Patel DS, Pathania M, van den Berg B, Im W, Kleinekathöfer U. Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-Negative Porin. The Journal of Physical Chemistry. B. PMID 31260306 DOI: 10.1021/Acs.Jpcb.9B03669 |
0.443 |
|
| 2019 |
Hughes AV, Patel DS, Widmalm G, Klauda JB, Clifton LA, Im W. Physical Properties of Bacterial Outer Membrane Models: Neutron Reflectometry & Molecular Simulation. Biophysical Journal. PMID 30850116 DOI: 10.1016/J.Bpj.2019.02.001 |
0.505 |
|
| 2019 |
Lee HS, Im W. Stalis: A Computational Method for Template-Based Ab Initio Ligand Design. Journal of Computational Chemistry. PMID 30829435 DOI: 10.1002/Jcc.25813 |
0.325 |
|
| 2019 |
Park S, Glover KJ, Im W. U-shaped caveolin-1 conformations are tightly regulated by hydrogen bonds with lipids. Journal of Computational Chemistry. PMID 30828836 DOI: 10.1002/Jcc.25807 |
0.424 |
|
| 2019 |
Park SJ, Lee J, Qi Y, Kern NR, Lee HS, Jo S, Joung I, Joo K, Lee J, Im W. CHARMM-GUI Glycan Modeler for Modeling and Simulation of Carbohydrates and Glycoconjugates. Glycobiology. PMID 30689864 DOI: 10.1093/Glycob/Cwz003 |
0.638 |
|
| 2019 |
Qi Y, Lee J, Klauda JB, Im W. CHARMM-GUI Nanodisc Builder for modeling and simulation of various nanodisc systems. Journal of Computational Chemistry. 40: 893-899. PMID 30677169 DOI: 10.1002/Jcc.25773 |
0.508 |
|
| 2019 |
Im W. Glycan Structure Modeling and Simulation Biophysical Journal. 116: 562a. DOI: 10.1016/J.Bpj.2018.11.3022 |
0.399 |
|
| 2019 |
Lee H, Im W. Molecular Dynamics Simulation Studies of the Interferon-Induced Transmembrane Protein (IFITM3) Biophysical Journal. 116: 432a. DOI: 10.1016/J.Bpj.2018.11.2328 |
0.423 |
|
| 2019 |
Gao Y, Lee J, Im W. Modeling and Simulation of Outer Membranes with LPS, ECAs, and CPs Biophysical Journal. 116: 365a. DOI: 10.1016/J.Bpj.2018.11.1987 |
0.417 |
|
| 2019 |
Lee J, Huang YJ, Montelione GT, Im W. Charmm-Gui NMR Structure Calculator: A Web-Based Tool for Calculating Biomolecular NMR Structures Biophysical Journal. 116: 289a. DOI: 10.1016/J.Bpj.2018.11.1559 |
0.324 |
|
| 2018 |
Kim S, Pires MM, Im W. Insight into Elongation Stages of Peptidoglycan Processing in Bacterial Cytoplasmic Membranes. Scientific Reports. 8: 17704. PMID 30531805 DOI: 10.1038/S41598-018-36075-Y |
0.475 |
|
| 2018 |
Lee J, Patel DS, Ståhle J, Park SJ, Kern NR, Kim SH, Lee J, Cheng X, Valvano MA, Holst O, Knirel YA, Qi Y, Jo S, Klauda JB, Widmalm G, ... Im W, et al. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. Journal of Chemical Theory and Computation. PMID 30525595 DOI: 10.1021/Acs.Jctc.8B01066 |
0.663 |
|
| 2018 |
Park S, Im W. Analysis of Lipid Order States and Domains in Lipid Bilayer Simulations. Journal of Chemical Theory and Computation. PMID 30468704 DOI: 10.1021/Acs.Jctc.8B00828 |
0.389 |
|
| 2018 |
Lee HS, Oh Y, Kim MJ, Im W. Molecular Basis of Aqueous-Like Activity of Lipase Treated with Glucose-Headed Surfactant in Organic Solvent. The Journal of Physical Chemistry. B. PMID 30398874 DOI: 10.1021/Acs.Jpcb.8B07686 |
0.334 |
|
| 2018 |
Dong C, Lee J, Kim S, Lai W, Webb EB, Oztekin A, Zhang XF, Im W. Long-ranged Protein-glycan Interactions Stabilize von Willebrand Factor A2 Domain from Mechanical Unfolding. Scientific Reports. 8: 16017. PMID 30375453 DOI: 10.1038/s41598-018-34374-y |
0.344 |
|
| 2018 |
Bang I, Kim HR, Beaven AH, Kim J, Ko SB, Lee GR, Lee H, Im W, Seok C, Chung KY, Choi HJ. Biophysical and functional characterization of Norrin signaling through Frizzled4. Proceedings of the National Academy of Sciences of the United States of America. PMID 30104375 DOI: 10.1073/Pnas.1805901115 |
0.306 |
|
| 2018 |
Lee J, Pothula KR, Kleinekathöfer U, Im W. Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes. The Journal of Physical Chemistry. B. PMID 30075620 DOI: 10.1021/Acs.Jpcb.8B07109 |
0.469 |
|
| 2018 |
Ren Z, Lee J, Moosa MM, Nian Y, Hu L, Xu Z, McCoy JG, Ferreon ACM, Im W, Zhou M. Structure of an EIIC sugar transporter trapped in an inward-facing conformation. Proceedings of the National Academy of Sciences of the United States of America. PMID 29784777 DOI: 10.1073/Pnas.1800647115 |
0.388 |
|
| 2018 |
Park S, Im W. Quantitative Characterization of Cholesterol Partitioning Between Binary Bilayers. Journal of Chemical Theory and Computation. PMID 29733641 DOI: 10.1021/Acs.Jctc.8B00140 |
0.446 |
|
| 2018 |
Min D, Jefferson RE, Qi Y, Wang JY, Arbing MA, Im W, Bowie JU. Unfolding of a ClC chloride transporter retains memory of its evolutionary history. Nature Chemical Biology. PMID 29581582 DOI: 10.1038/S41589-018-0025-4 |
0.395 |
|
| 2018 |
Park S, Krshnan L, Call MJ, Call ME, Im W. Structural Conservation and Effects of Alterations in T Cell Receptor Transmembrane Interfaces. Biophysical Journal. PMID 29395047 DOI: 10.1016/J.Bpj.2018.01.004 |
0.421 |
|
| 2018 |
Park S, Sun Lee H, Lee J, Im W. Computational Toolset for Glycoconjugate Modeling and Simulation Biophysical Journal. 114: 680a. DOI: 10.1016/J.Bpj.2017.11.3669 |
0.337 |
|
| 2018 |
Feng S, Klauda JB, Im W. Function, Property, and Interaction of Archaeal Lipids: A Molecular Dynamics Simulation Study Biophysical Journal. 114: 459a. DOI: 10.1016/J.Bpj.2017.11.2534 |
0.444 |
|
| 2018 |
Lee J, Widmalm G, Klauda JB, Im W. Charmm-GUI Membrane Builder with Glycolipids and Lipopolysaccharides Biophysical Journal. 114: 344a. DOI: 10.1016/J.Bpj.2017.11.1920 |
0.374 |
|
| 2018 |
Kim S, Pires M, Im W. Molecular Dynamics Simulation Studies of Polymyxin B Derivatives in Homogeneous E. coli K12 Bilayers Biophysical Journal. 114: 341a. DOI: 10.1016/J.Bpj.2017.11.1902 |
0.354 |
|
| 2018 |
Lee J, Im W. Modeling and Simulation of Outer Membrane Proteins in Pseudomonas Aeruginosa Outer Membranes Biophysical Journal. 114: 241a. DOI: 10.1016/J.Bpj.2017.11.1344 |
0.446 |
|
| 2018 |
Im W. A (Passive to Active) Chaser: NMR and MD of Membrane Proteins Biophysical Journal. 114: 206a. DOI: 10.1016/J.Bpj.2017.11.1156 |
0.404 |
|
| 2018 |
Kern NR, Lee J, Fine-Morris M, Klauda JB, Kuczera K, Fleming P, Im W. CHARMM-GUI Lecture Series on Molecular Modeling and Simulation Biophysical Journal. 114: 184a. DOI: 10.1016/J.Bpj.2017.11.1027 |
0.384 |
|
| 2017 |
Jo S, Myatt D, Qi Y, Doutch J, Clifton LA, Im W, Widmalm G. Multiple Conformational States Contribute to the 3D Structure of a Glucan Decasaccharide: A Combined SAXS and MD Simulation Study. The Journal of Physical Chemistry. B. PMID 29268602 DOI: 10.1021/Acs.Jpcb.7B11085 |
0.626 |
|
| 2017 |
Lee HS, Im W. Effects of N-Glycan Composition on Structure and Dynamics of IgG1 Fc and Their Implications for Antibody Engineering. Scientific Reports. 7: 12659. PMID 28978918 DOI: 10.1038/S41598-017-12830-5 |
0.32 |
|
| 2017 |
Machen AJ, Akkaladevi N, Trecazzi C, O'Neil PT, Mukherjee S, Qi Y, Dillard R, Im W, Gogol EP, White TA, Fisher MT. Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain. Toxins. 9. PMID 28937604 DOI: 10.3390/Toxins9100298 |
0.331 |
|
| 2017 |
Beaven AH, Sodt AJ, Pastor RW, Koeppe RE, Andersen OS, Im W. Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes. Journal of Chemical Theory and Computation. PMID 28870079 DOI: 10.1021/Acs.Jctc.7B00400 |
0.38 |
|
| 2017 |
Hsu PC, Bruininks BMH, Jefferies D, Cesar Telles de Souza P, Lee J, Patel DS, Marrink SJ, Qi Y, Khalid S, Im W. CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. Journal of Computational Chemistry. PMID 28776689 DOI: 10.1002/Jcc.24895 |
0.492 |
|
| 2017 |
Matthias KA, Strader MB, Nawar HF, Gao YS, Lee J, Patel DS, Im W, Bash MC. 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. Molecular Microbiology. PMID 28708335 DOI: 10.1111/Mmi.13747 |
0.367 |
|
| 2017 |
Blasco P, Patel DS, Engström O, Im W, Widmalm G. Conformational dynamics of the lipopolysaccharide from Escherichia coli O91 revealed by NMR spectroscopy and molecular simulations. Biochemistry. PMID 28609625 DOI: 10.1021/Acs.Biochem.7B00106 |
0.393 |
|
| 2017 |
Park SJ, Lee J, Patel DS, Ma H, Lee HS, Jo S, Im W. Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank. Bioinformatics (Oxford, England). PMID 28582506 DOI: 10.1093/Bioinformatics/Btx358 |
0.572 |
|
| 2017 |
Sun Lee H, Im W. Transmembrane Motions of PglB Induced by LLO are Coupled with EL5 Loop Conformational Changes Necessary for OST Activity. Glycobiology. PMID 28575441 DOI: 10.1093/Glycob/Cwx052 |
0.42 |
|
| 2017 |
Lee J, Ren Z, Zhou M, Im W. Molecular Simulation and Biochemical Studies Support an Elevator-Type Transport Mechanism in EIIC. Biophysical Journal. PMID 28506526 DOI: 10.1016/J.Bpj.2017.04.040 |
0.441 |
|
| 2017 |
Kim S, Lee J, Jo S, Brooks CL, Lee HS, Im W. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. Journal of Computational Chemistry. PMID 28497616 DOI: 10.1002/Jcc.24829 |
0.608 |
|
| 2017 |
Lee HS, Im W. G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures. Methods in Molecular Biology (Clifton, N.J.). 1611: 97-108. PMID 28451974 DOI: 10.1007/978-1-4939-7015-5_8 |
0.354 |
|
| 2017 |
Sodt AJ, Beaven AH, Andersen OS, Im W, Pastor RW. Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model. Biophysical Journal. 112: 1198-1213. PMID 28355547 DOI: 10.1016/J.Bpj.2017.01.035 |
0.412 |
|
| 2017 |
Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W. Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. Biophysical Journal. 112: 1185-1197. PMID 28355546 DOI: 10.1016/J.Bpj.2017.01.028 |
0.549 |
|
| 2017 |
Patel DS, Qi Y, Im W. Modeling and simulation of bacterial outer membranes and interactions with membrane proteins. Current Opinion in Structural Biology. 43: 131-140. PMID 28157627 DOI: 10.1016/J.Sbi.2017.01.003 |
0.448 |
|
| 2017 |
Lee J, Patel DS, Kucharska I, Tamm LK, Im W. Refinement of OprH-LPS Interactions by Molecular Simulations. Biophysical Journal. 112: 346-355. PMID 28122220 DOI: 10.1016/J.Bpj.2016.12.006 |
0.405 |
|
| 2017 |
Lee J, Ren Z, Zhou M, Im W. Molecular Dynamics Studies Support Elevator Type Transport Mechanisms in the Glucose EIIC Superfamily Transporters Biophysical Journal. 112: 138a-139a. DOI: 10.1016/J.Bpj.2016.11.767 |
0.359 |
|
| 2017 |
Ren Z, Nian Y, Lee J, McCoy J, Im W, Zhou M. Elevator-Like Mechanism of Transport in the EIIC Glucose Superfamily of Transporters Biophysical Journal. 112: 128a-129a. DOI: 10.1016/J.Bpj.2016.11.716 |
0.358 |
|
| 2017 |
Park S, Im W. Analysis of Lipid Domains in Bilayer Simulations using Observables for Lipid Packing Biophysical Journal. 112: 81a. DOI: 10.1016/J.Bpj.2016.11.483 |
0.439 |
|
| 2017 |
Kim S, Im W. Molecular Dynamics Simulations of 38 Types of Ganglioside in Homoegneous Membrane Bilayers Biophysical Journal. 112: 74a. DOI: 10.1016/J.Bpj.2016.11.444 |
0.503 |
|
| 2017 |
Beaven AH, Sodt AJ, Pastor RW, Im W. Protocol and Validation of CHARMM-GUI Hex Phase Builder Biophysical Journal. 112: 73a-74a. DOI: 10.1016/J.Bpj.2016.11.442 |
0.416 |
|
| 2017 |
Ma H, Lee J, Im W. Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 having N-Glycans and Heparan Sulfates in Membranes Biophysical Journal. 112: 390a. DOI: 10.1016/J.Bpj.2016.11.2119 |
0.477 |
|
| 2017 |
Kim S, Lee J, Jo S, Im W. CHARMM-GUI Ligand Reader & Modeler Biophysical Journal. 112: 289a. DOI: 10.1016/J.Bpj.2016.11.1564 |
0.606 |
|
| 2016 |
Qi Y, Lee J, Singharoy A, Mcgreevy R, Schulten K, Im W. CHRAMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. The Journal of Physical Chemistry. B. PMID 27936734 DOI: 10.1021/Acs.Jpcb.6B10568 |
0.472 |
|
| 2016 |
Jo S, Cheng X, Lee J, Kim S, Park SJ, Patel DS, Beaven AH, Lee KI, Rui H, Park S, Lee HS, Roux B, MacKerell AD, Klauda JB, Qi Y, ... Im W, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry. PMID 27862047 DOI: 10.1002/Jcc.24660 |
0.773 |
|
| 2016 |
Patel DS, Park S, Wu EL, Yeom MS, Widmalm G, Klauda JB, Im W. Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature. Biophysical Journal. 111: 1987-1999. PMID 27806280 DOI: 10.1016/J.Bpj.2016.09.021 |
0.415 |
|
| 2016 |
Krshnan L, Park S, Im W, Call MJ, Call ME. A conserved αβ transmembrane interface forms the core of a compact T-cell receptor-CD3 structure within the membrane. Proceedings of the National Academy of Sciences of the United States of America. 113: E6649-E6658. PMID 27791034 DOI: 10.1073/Pnas.1611445113 |
0.359 |
|
| 2016 |
Boughter CT, Monje-Galvan V, Im W, Klauda JB. Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics. The Journal of Physical Chemistry. B. PMID 27771953 DOI: 10.1021/Acs.Jpcb.6B08574 |
0.434 |
|
| 2016 |
Kim S, Patel DS, Park S, Slusky J, Klauda JB, Widmalm G, Im W. Bilayer Properties of Lipid A from Various Gram-Negative Bacteria. Biophysical Journal. 111: 1750-1760. PMID 27760361 DOI: 10.1016/J.Bpj.2016.09.001 |
0.408 |
|
| 2016 |
Qi Y, Klauda JB, Im W. Effects of Spin-Labels on Membrane Burial Depth of MARCKS-ED Residues. Biophysical Journal. PMID 27692366 DOI: 10.1016/J.Bpj.2016.09.013 |
0.326 |
|
| 2016 |
Zhuang X, Dávila-Contreras EM, Beaven AH, Im W, Klauda JB. An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations. Biochimica Et Biophysica Acta. PMID 27664502 DOI: 10.1016/J.Bbamem.2016.09.016 |
0.393 |
|
| 2016 |
Fleming PJ, Patel DS, Wu EL, Qi Y, Yeom MS, Sousa MC, Fleming KG, Im W. BamA POTRA Domain Interacts with a Native Lipid Membrane Surface. Biophysical Journal. 110: 2698-709. PMID 27332128 DOI: 10.1016/J.Bpj.2016.05.010 |
0.446 |
|
| 2016 |
Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. Journal of Molecular Biology. PMID 27255863 DOI: 10.1016/J.Jmb.2016.05.024 |
0.398 |
|
| 2016 |
McCoy JG, Ren Z, Stanevich V, Lee J, Mitra S, Levin EJ, Poget S, Quick M, Im W, Zhou M. The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport. Structure (London, England : 1993). PMID 27161976 DOI: 10.1016/J.Str.2016.04.003 |
0.358 |
|
| 2016 |
Kumar R, Qi Y, Matsumura H, Lovell SW, Yao H, Battaile KP, Im W, Moënne-Loccoz P, Rivera M. Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein. Biochemistry. PMID 27074415 DOI: 10.1021/Acs.Biochem.6B00239 |
0.31 |
|
| 2016 |
Patel DS, Re S, Wu EL, Qi Y, Klebba PE, Widmalm G, Yeom MS, Sugita Y, Im W. Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. Biophysical Journal. 110: 930-8. PMID 26910429 DOI: 10.1016/J.Bpj.2016.01.002 |
0.4 |
|
| 2016 |
Lee HS, Im W. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design. Protein Science : a Publication of the Protein Society. PMID 26813336 DOI: 10.1002/Pro.2890 |
0.329 |
|
| 2016 |
Mori T, Miyashita N, Im W, Feig M, Sugita Y. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms. Biochimica Et Biophysica Acta. PMID 26766517 DOI: 10.1016/J.Bbamem.2015.12.032 |
0.522 |
|
| 2016 |
Ren Z, McCoy JG, Stanevich V, Lee J, Mitra S, Levin EJ, Poget S, Quick M, Im W, Zhou M. Transport Mechanism of the EIIC Glucose Superfamily of Transporters Biophysical Journal. 110: 178a. DOI: 10.1016/J.Bpj.2015.11.995 |
0.34 |
|
| 2016 |
Islam SM, Florin G, Qi Y, Shen R, Han W, Stein RA, Schulten K, Mchaourab HS, Im W, Roux B. Structural-Function Study of Membrane Proteins with Restrained-Ensemble and Dummy Spin-Label Molecular Dynamics Simulations Biophysical Journal. 110: 644a. DOI: 10.1016/J.Bpj.2015.11.3446 |
0.569 |
|
| 2016 |
Shin J, Im W. CHARMM Molecular Dynamics of the Blood Group Glycolipids in Popc Lipid Bilayer Biophysical Journal. 110: 328a. DOI: 10.1016/J.Bpj.2015.11.1763 |
0.408 |
|
| 2016 |
Malladi V, Im W. CHARMM-GUI Molecular Dynamics Simulations of the Neo-Lacto Series in a Popc Bilayer Biophysical Journal. 110: 328a. DOI: 10.1016/J.Bpj.2015.11.1762 |
0.467 |
|
| 2016 |
Kim S, Im W. Molecular Dynamics Simulation Studies of Membrane Bilayers of Lipid a from Various Gram-Negative Bacteria Biophysical Journal. 110: 323a. DOI: 10.1016/J.Bpj.2015.11.1735 |
0.455 |
|
| 2016 |
Itagi P, Im W. Molecular Dynamics Simulation Studies of Lipopolysaccharide Micelles Biophysical Journal. 110: 323a. DOI: 10.1016/J.Bpj.2015.11.1734 |
0.376 |
|
| 2016 |
Kim S, Im W. Molecular Dynamics Simulations of 41 Types of Ganglioside in Membrane Bilayers Biophysical Journal. 110: 322a-323a. DOI: 10.1016/J.Bpj.2015.11.1732 |
0.493 |
|
| 2015 |
Cheng X, Kim JK, Kim Y, Bowie JU, Im W. Molecular dynamics simulation strategies for protein-micelle complexes. Biochimica Et Biophysica Acta. PMID 26679426 DOI: 10.1016/J.Bbamem.2015.12.012 |
0.47 |
|
| 2015 |
Lee JH, Oh M, Kim HS, Lee HS, Im W, Lim HS. Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions. Acs Combinatorial Science. PMID 26651509 DOI: 10.1021/Acscombsci.5B00080 |
0.305 |
|
| 2015 |
Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, ... ... Im W, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935 |
0.657 |
|
| 2015 |
Wu EL, Qi Y, Park S, Mallajosyula SS, MacKerell AD, Klauda JB, Im W. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophysical Journal. 109: 2090-2100. PMID 26588568 DOI: 10.1016/J.Bpj.2015.10.009 |
0.456 |
|
| 2015 |
Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, Im W. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophysical Journal. 109: 2012-2022. PMID 26588561 DOI: 10.1016/J.Bpj.2015.10.008 |
0.484 |
|
| 2015 |
Lee HS, Seok C, Im W. Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy. Journal of Chemical Theory and Computation. 11: 1255-1266. PMID 26579772 DOI: 10.1021/Ct5008907 |
0.342 |
|
| 2015 |
Qi Y, Ingólfsson HI, Cheng X, Lee J, Marrink SJ, Im W. CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field. Journal of Chemical Theory and Computation. 11: 4486-4494. PMID 26575938 DOI: 10.1021/Acs.Jctc.5B00513 |
0.45 |
|
| 2015 |
Park S, Beaven AH, Klauda JB, Im W. How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets? Journal of Chemical Theory and Computation. 11: 3466-3477. PMID 26575780 DOI: 10.1021/Acs.Jctc.5B00232 |
0.47 |
|
| 2015 |
Qi Y, Jo S, Im W. Roles of Glycans in Interactions between gp120 and HIV Broadly Neutralizing Antibodies. Glycobiology. PMID 26537503 DOI: 10.1093/Glycob/Cwv101 |
0.548 |
|
| 2015 |
Jo S, Qi Y, Im W. Preferred Conformations of N-glycan Core Pentasaccharide in Solution and in Glycoproteins. Glycobiology. PMID 26405106 DOI: 10.1093/Glycob/Cwv083 |
0.627 |
|
| 2015 |
Knoblich K, Park S, Lutfi M, van 't Hag L, Conn CE, Seabrook SA, Newman J, Czabotar PE, Im W, Call ME, Call MJ. Transmembrane Complexes of DAP12 Crystallized in Lipid Membranes Provide Insights into Control of Oligomerization in Immunoreceptor Assembly. Cell Reports. 11: 1184-92. PMID 25981043 DOI: 10.1016/J.Celrep.2015.04.045 |
0.425 |
|
| 2015 |
Cheng X, Jo S, Qi Y, Marassi FM, Im W. Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes. Biophysical Journal. 108: 1954-62. PMID 25902435 DOI: 10.1016/J.Bpj.2015.03.012 |
0.7 |
|
| 2015 |
Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W. GS-align for glycan structure alignment and similarity measurement. Bioinformatics (Oxford, England). PMID 25857669 DOI: 10.1093/Bioinformatics/Btv202 |
0.597 |
|
| 2015 |
Mallajosyula SS, Jo S, Im W, MacKerell AD. Molecular dynamics simulations of glycoproteins using CHARMM. Methods in Molecular Biology (Clifton, N.J.). 1273: 407-29. PMID 25753723 DOI: 10.1007/978-1-4939-2343-4_25 |
0.651 |
|
| 2015 |
Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Widmalm G, Im W. Lipopolysaccharide membrane building and simulation. Methods in Molecular Biology (Clifton, N.J.). 1273: 391-406. PMID 25753722 DOI: 10.1007/978-1-4939-2343-4_24 |
0.677 |
|
| 2015 |
Lee HS, Qi Y, Im W. Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study. Scientific Reports. 5: 8926. PMID 25748215 DOI: 10.1038/Srep08926 |
0.404 |
|
| 2015 |
Yao H, Rui H, Kumar R, Eshelman K, Lovell S, Battaile KP, Im W, Rivera M. Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry. 54: 1611-27. PMID 25640193 DOI: 10.1021/Bi501255R |
0.551 |
|
| 2015 |
Qi Y, Cheng X, Im W. CHARMM-GUI Martini Maker for Coarse-Grained Simulations Biophysical Journal. 108: 161a. DOI: 10.1016/J.Bpj.2014.11.888 |
0.431 |
|
| 2015 |
Cheng X, Qi Y, Lee J, Jo S, Im W. CHARMM Gui Membrane Builder Updates Biophysical Journal. 108: 159a. DOI: 10.1016/J.Bpj.2014.11.877 |
0.648 |
|
| 2015 |
Lee HS, Im W. G-Losa: An Efficient Computational Tool for Local Structure-Centric Biological Studies Biophysical Journal. 108: 473a. DOI: 10.1016/J.Bpj.2014.11.2584 |
0.356 |
|
| 2015 |
Park S, Im W. Effect of Asymmetry on Bilayer Membrane Systems Biophysical Journal. 108: 467a. DOI: 10.1016/J.Bpj.2014.11.2553 |
0.456 |
|
| 2015 |
Lee J, Im W. Molecular Dynamics Studies for the Sugar Transportation Mechanism in Phosphotransferase Systems (PTSS) Biophysical Journal. 108: 467a. DOI: 10.1016/J.Bpj.2014.11.2552 |
0.404 |
|
| 2015 |
Kim S, Im W. Molecular Dynamics Studies of Lipid I and Lipid II in Various of Lipid Bilayer Environments Biophysical Journal. 108: 412a. DOI: 10.1016/J.Bpj.2014.11.2261 |
0.389 |
|
| 2015 |
Im W. Bacterial Outer Membranes and Interactions with Membrane Proteins Biophysical Journal. 108: 370a. DOI: 10.1016/J.Bpj.2014.11.2030 |
0.427 |
|
| 2015 |
Patel DS, Wu EL, Klebba PE, Im W. Molecular Dynamics Simulation Studies of Interactions of E. coli-K12 with OmpF in Outer Membranes: Effects of LPS Structures on Monoclonal Antibodies Binding Biophysical Journal. 108: 249a. DOI: 10.1016/J.Bpj.2014.11.1377 |
0.464 |
|
| 2015 |
Boyd TS, Im W. Modeling and Simulations of Glycosphingolipids Determining A, B, and O Blood Groups Biophysical Journal. 108: 243a. DOI: 10.1016/J.Bpj.2014.11.1345 |
0.339 |
|
| 2015 |
Beaven AH, Sodt AJ, Andersen OS, Pastor RW, Im W. Ion Channel Regulation by Lipid Bilayers: Theory & Simulation of Deformed Membranes around Gramicidin A Biophysical Journal. 108: 209a. DOI: 10.1016/J.Bpj.2014.11.1155 |
0.446 |
|
| 2014 |
Lee KI, Im W, Pastor RW. 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 Biophysics. 7: 13. PMID 25774289 DOI: 10.1186/S13628-014-0013-3 |
0.485 |
|
| 2014 |
Jo S, Cheng X, Islam SM, Huang L, Rui H, Zhu A, Lee HS, Qi Y, Han W, Vanommeslaeghe K, MacKerell AD, Roux B, Im W. CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Advances in Protein Chemistry and Structural Biology. 96: 235-65. PMID 25443960 DOI: 10.1016/Bs.Apcsb.2014.06.002 |
0.755 |
|
| 2014 |
Kern NR, Lee HS, Wu EL, Park S, Vanommeslaeghe K, MacKerell AD, Klauda JB, Jo S, Im W. Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase. Biophysical Journal. 107: 1885-95. PMID 25418169 DOI: 10.1016/J.Bpj.2014.09.007 |
0.692 |
|
| 2014 |
Wu EL, Cheng X, Jo S, Rui H, Song KC, Dávila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W. CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. Journal of Computational Chemistry. 35: 1997-2004. PMID 25130509 DOI: 10.1002/Jcc.23702 |
0.815 |
|
| 2014 |
Oh M, Lee JH, Wang W, Lee HS, Lee WS, Burlak C, Im W, Hoang QQ, Lim HS. Potential pharmacological chaperones targeting cancer-associated MCL-1 and Parkinson disease-associated α-synuclein. Proceedings of the National Academy of Sciences of the United States of America. 111: 11007-12. PMID 25024216 DOI: 10.1073/Pnas.1320556111 |
0.309 |
|
| 2014 |
Zhuang X, Makover JR, Im W, Klauda JB. A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties. Biochimica Et Biophysica Acta. 1838: 2520-9. PMID 24953542 DOI: 10.1016/J.Bbamem.2014.06.010 |
0.44 |
|
| 2014 |
Wu EL, Fleming PJ, Yeom MS, Widmalm G, Klauda JB, Fleming KG, Im W. E. coli outer membrane and interactions with OmpLA. Biophysical Journal. 106: 2493-502. PMID 24896129 DOI: 10.1016/J.Bpj.2014.04.024 |
0.464 |
|
| 2014 |
Wu EL, Qi Y, Song KC, Klauda JB, Im W. Preferred orientations of phosphoinositides in bilayers and their implications in protein recognition mechanisms. The Journal of Physical Chemistry. B. 118: 4315-25. PMID 24689790 DOI: 10.1021/Jp500610T |
0.697 |
|
| 2014 |
Rui H, Root KT, Lee J, Glover KJ, Im W. Probing the U-shaped conformation of caveolin-1 in a bilayer. Biophysical Journal. 106: 1371-80. PMID 24655512 DOI: 10.1016/J.Bpj.2014.02.005 |
0.65 |
|
| 2014 |
Jeong JC, Jo S, Wu EL, Qi Y, Monje-Galvan V, Yeom MS, Gorenstein L, Chen F, Klauda JB, Im W. ST-analyzer: a web-based user interface for simulation trajectory analysis. Journal of Computational Chemistry. 35: 957-63. PMID 24638223 DOI: 10.1002/Jcc.23584 |
0.648 |
|
| 2014 |
Qi Y, Cheng X, Han W, Jo S, Schulten K, Im W. CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations. Journal of Chemical Information and Modeling. 54: 1003-9. PMID 24624945 DOI: 10.1021/Ci500007N |
0.662 |
|
| 2014 |
Li PC, Miyashita N, Im W, Ishido S, Sugita Y. Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. Journal of Computational Chemistry. 35: 300-8. PMID 24258786 DOI: 10.1002/Jcc.23494 |
0.474 |
|
| 2014 |
Davila Contreras EM, Beaven AH, Klauda JB, Im W. Characterization of Pure Lipid Bilayers using Molecular Dynamics Simulations Biophysical Journal. 106: 81a. DOI: 10.1016/J.Bpj.2013.11.523 |
0.462 |
|
| 2014 |
Qi Y, Cheng X, Han W, Jo S, Roux B, Schulten K, Im W. CHARMM-Gui Pace Cg Builder for Solution, Micelle, Bilayer and Vesicle Simulations Biophysical Journal. 106: 809a. DOI: 10.1016/J.Bpj.2013.11.4437 |
0.698 |
|
| 2014 |
Park S, Im W. Quantitative Characterization of Membrane Protein-Lipid Interactions Biophysical Journal. 106: 805a. DOI: 10.1016/J.Bpj.2013.11.4413 |
0.45 |
|
| 2014 |
Lee HS, Im W. A Thermodynamic Discrimination of Efficacy of GPCR Ligands using Absolute Binding Free Energy Calculations Biophysical Journal. 106: 804a. DOI: 10.1016/J.Bpj.2013.11.4410 |
0.342 |
|
| 2014 |
Cheng X, Im W. NMR-Based Explicit Ensemble Dynamics Simulations of Membrane Protein Biophysical Journal. 106: 802a. DOI: 10.1016/J.Bpj.2013.11.4396 |
0.491 |
|
| 2014 |
Im W. A Molecular Dynamics Simulation Study of Lipid-Linked Peptidoglycan Precursors in Lipid Bilayers Biophysical Journal. 106: 802a. DOI: 10.1016/J.Bpj.2013.11.4394 |
0.401 |
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| 2014 |
Beaven AH, Sodt AJ, Greathouse DV, Koeppe RE, Pastor RW, Andersen OS, Im W. All-Atom Simulation and Continuum Elastic Theory of Gramicidin a in Binary Component Lipid Bilayers Biophysical Journal. 106: 801a. DOI: 10.1016/J.Bpj.2013.11.4389 |
0.366 |
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| 2014 |
Kern NR, Wu EL, Jo S, Vanommeslaeghe K, Im W. Molecular Dynamics Simulations of Lipid-Linked Oligosaccharides in Lipid Bilayers Biophysical Journal. 106: 703a. DOI: 10.1016/J.Bpj.2013.11.3892 |
0.69 |
|
| 2014 |
Wu EL, Fleming PJ, Klauda JB, Fleming KG, Im W. A Molecular Dynamics Simulation Study of Outer Membrane Phospholipase a (OMPLA) Structure and Dynamics in an Asymmetric Lipopolysaccharide Membrane Biophysical Journal. 106: 656a. DOI: 10.1016/J.Bpj.2013.11.3632 |
0.497 |
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| 2014 |
Rui H, Root KT, Lee J, Glover KJ, Im W. Caveolin in Bilayers: Can the Intramembrane U-Shaped Conformation Really Exist Biophysical Journal. 106: 641a. DOI: 10.1016/J.Bpj.2013.11.3547 |
0.644 |
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| 2014 |
Lee J, Im W. Molecular Dynamics Studies: The Effect of Phosphorylation in Saccharide Transporter System Biophysical Journal. 106: 610a. DOI: 10.1016/J.Bpj.2013.11.3376 |
0.353 |
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| 2014 |
McCoy JG, Mitra S, Levin EJ, Huang H, Lee J, Im W, Quick M, Kloss B, Bruni R, Zhou M. Structure and Function of a Phosphorylation-Coupled Saccharide Transporter Biophysical Journal. 106: 368a. DOI: 10.1016/J.Bpj.2013.11.2085 |
0.384 |
|
| 2013 |
Qi Y, Im W. Quantification of Drive-Response Relationships Between Residues During Protein Folding. Journal of Chemical Theory and Computation. 9. PMID 24223527 DOI: 10.1021/Ct4002784 |
0.363 |
|
| 2013 |
Wu EL, Engström O, Jo S, Stuhlsatz D, Yeom MS, Klauda JB, Widmalm G, Im W. Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics. Biophysical Journal. 105: 1444-55. PMID 24047996 DOI: 10.1016/J.Bpj.2013.08.002 |
0.638 |
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| 2013 |
Lee HS, Im W. Ligand binding site detection by local structure alignment and its performance complementarity. Journal of Chemical Information and Modeling. 53: 2462-70. PMID 23957286 DOI: 10.1021/Ci4003602 |
0.328 |
|
| 2013 |
Cheng X, Jo S, Marassi FM, Im W. NMR-based simulation studies of Pf1 coat protein in explicit membranes. Biophysical Journal. 105: 691-8. PMID 23931317 DOI: 10.1016/J.Bpj.2013.06.040 |
0.699 |
|
| 2013 |
Cheng X, Jo S, Lee HS, Klauda JB, Im W. CHARMM-GUI micelle builder for pure/mixed micelle and protein/micelle complex systems. Journal of Chemical Information and Modeling. 53: 2171-80. PMID 23865552 DOI: 10.1021/Ci4002684 |
0.655 |
|
| 2013 |
Jo S, Lee HS, Skolnick J, Im W. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. Plos Computational Biology. 9: e1002946. PMID 23516343 DOI: 10.1371/Journal.Pcbi.1002946 |
0.603 |
|
| 2013 |
Park S, Im W. Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly. Journal of Chemical Theory and Computation. 9: 13-17. PMID 23486635 DOI: 10.1021/Ct3008556 |
0.35 |
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| 2013 |
Lee KI, Pastor RW, Andersen OS, Im W. Assessing smectic liquid-crystal continuum models for elastic bilayer deformations. Chemistry and Physics of Lipids. 169: 19-26. PMID 23348553 DOI: 10.1016/J.Chemphyslip.2013.01.005 |
0.466 |
|
| 2013 |
Jo S, Jiang W, Lee HS, Roux B, Im W. CHARMM-GUI Ligand Binder for absolute binding free energy calculations and its application. Journal of Chemical Information and Modeling. 53: 267-77. PMID 23205773 DOI: 10.1021/Ci300505N |
0.655 |
|
| 2013 |
Jo S, Im W. Glycan fragment database: a database of PDB-based glycan 3D structures. Nucleic Acids Research. 41: D470-4. PMID 23104379 DOI: 10.1093/Nar/Gks987 |
0.581 |
|
| 2013 |
Park S, Im W. Window Exchange Umbrella Sampling to Enhance Conformational Sampling and Quantify Energetics in Transmembrane Helix Assembly Biophysical Journal. 104: 170a. DOI: 10.1016/J.Bpj.2012.11.957 |
0.324 |
|
| 2013 |
Rui H, Kossiakoff AA, Im W. Structural Modeling of Human Growth Hormone Receptor using Computational Simulations and NMR Spectroscopy Biophysical Journal. 104: 117a-118a. DOI: 10.1016/J.Bpj.2012.11.678 |
0.597 |
|
| 2013 |
Kern N, Wu EL, Jo S, Vanommeslaeghe K, Im W. Molecular Dynamics Simulations of Lipid-Linked Oligosaccharide in Membrane Bilayers Biophysical Journal. 104: 83a. DOI: 10.1016/J.Bpj.2012.11.498 |
0.692 |
|
| 2013 |
Mukherjee S, Lee KI, Zhang Y, Fisher M, Im W. Modeling, Ion Conductance, and Electrostatic Properties of the Protective Antigen Pore Structure of Anthrax Toxin Biophysical Journal. 104: 63a. DOI: 10.1016/J.Bpj.2012.11.386 |
0.415 |
|
| 2013 |
Monje V, Kim T, Im W, Klauda JB. Improved Charmm Force Field for Polyunsaturated Fatty Acid Chains, a Study on DAPC Membranes Biophysical Journal. 104: 590a. DOI: 10.1016/J.Bpj.2012.11.3277 |
0.568 |
|
| 2013 |
Beaven AH, Pastor RW, Andersen OS, Im W. Exploring Protein-Lipid Interactions using Gramicidin a as a Model System Biophysical Journal. 104: 432a-433a. DOI: 10.1016/J.Bpj.2012.11.2406 |
0.397 |
|
| 2013 |
Rui H, Jebrell Glover K, Im W. Molecular Dynamics Simulations of Caveolin-1 in Membrane Bilayers Biophysical Journal. 104: 410a. DOI: 10.1016/J.Bpj.2012.11.2287 |
0.633 |
|
| 2013 |
Sun Lee H, Im W. Computer-Aided Drug Design Utilizing Structure Templates Identified by Local Structure Alignment Biophysical Journal. 104: 404a-405a. DOI: 10.1016/J.Bpj.2012.11.2257 |
0.33 |
|
| 2013 |
Qi Y, Im W. Quantifying the Drive-Response Relationships between Residues in Protein Folding Biophysical Journal. 104: 398a. DOI: 10.1016/J.Bpj.2012.11.2219 |
0.361 |
|
| 2013 |
Cheol Jeong J, Jo S, Song K, Cheng X, Sun Lee H, Klauda JB, Im W. Introduction of Membrane Analyzer and Updates of Membrane Builder Biophysical Journal. 104: 335a. DOI: 10.1016/J.Bpj.2012.11.1865 |
0.778 |
|
| 2013 |
Jo S, sun Lee H, Li G, Skolnick J, Im W. N-Glycan Structure Modeling and in Silico Glycosylation: Template-Based Structure Prediction of Carbohydrate Structures of Glycoconjugates Biophysical Journal. 104: 230a. DOI: 10.1016/J.Bpj.2012.11.1297 |
0.582 |
|
| 2013 |
Cheng X, Jo S, Im W. Computational Studies of Membrane Protein Based on NMR Observables Biophysical Journal. 104: 221a-222a. DOI: 10.1016/J.Bpj.2012.11.1249 |
0.683 |
|
| 2012 |
Rui H, Rivera M, Im W. Protein dynamics and ion traffic in bacterioferritin. Biochemistry. 51: 9900-10. PMID 23167635 DOI: 10.1021/Bi3013388 |
0.568 |
|
| 2012 |
Lee HS, Im W. Identification of ligand templates using local structure alignment for structure-based drug design. Journal of Chemical Information and Modeling. 52: 2784-95. PMID 22978550 DOI: 10.1021/Ci300178E |
0.329 |
|
| 2012 |
Lee HS, Jo S, Lim HS, Im W. Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors. Journal of Chemical Information and Modeling. 52: 1821-32. PMID 22731511 DOI: 10.1021/Ci3000997 |
0.597 |
|
| 2012 |
Klauda JB, Monje V, Kim T, Im W. Improving the CHARMM force field for polyunsaturated fatty acid chains. The Journal of Physical Chemistry. B. 116: 9424-31. PMID 22697583 DOI: 10.1021/Jp304056P |
0.529 |
|
| 2012 |
Cheng X, Im W. NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes. Biophysical Journal. 102: L27-9. PMID 22500771 DOI: 10.1016/J.Bpj.2012.03.002 |
0.495 |
|
| 2012 |
Kim T, Lee KI, Morris P, Pastor RW, Andersen OS, Im W. Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers. Biophysical Journal. 102: 1551-60. PMID 22500755 DOI: 10.1016/J.Bpj.2012.03.014 |
0.579 |
|
| 2012 |
Park S, Kim T, Im W. Transmembrane helix assembly by window exchange umbrella sampling. Physical Review Letters. 108: 108102. PMID 22463457 DOI: 10.1103/Physrevlett.108.108102 |
0.479 |
|
| 2012 |
Lee KI, Jo S, Rui H, Egwolf B, Roux B, Pastor RW, Im W. Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores. Journal of Computational Chemistry. 33: 331-9. PMID 22102176 DOI: 10.1002/Jcc.21952 |
0.748 |
|
| 2012 |
Im W, Jo S, Kim T. An ensemble dynamics approach to decipher solid-state NMR observables of membrane proteins. Biochimica Et Biophysica Acta. 1818: 252-62. PMID 21851810 DOI: 10.1016/J.Bbamem.2011.07.048 |
0.731 |
|
| 2012 |
Jo S, Im W. Glycan Builder for in Silico Glycosylation: Template-Based Structure Prediction of Carbohydrate Structures of Glycoconjugates Biophysical Journal. 102: 172a. DOI: 10.1016/J.Bpj.2011.11.933 |
0.61 |
|
| 2012 |
Song KC, Venable RM, Maliniak A, Im W, Gawrisch K, Pastor RW. Molecular Dynamics Simulation, 31P-NMR Spectroscopy, and Microelectrophoretic Studies of Cardiolipin Bilayers Biophysical Journal. 102: 97a. DOI: 10.1016/J.Bpj.2011.11.551 |
0.681 |
|
| 2012 |
Balijepalli A, Il Lee K, Im W, Pastor RW. Modeling Polymer Interactions with Nanopores for DNA Sequencing and Proteomics Applications Biophysical Journal. 102: 732a. DOI: 10.1016/J.Bpj.2011.11.3970 |
0.411 |
|
| 2012 |
Rui H, Im W. Turning on the Human Growth Hormone Receptor: A Computational Study on its Structure and Activation Mechanism Biophysical Journal. 102: 667a. DOI: 10.1016/J.Bpj.2011.11.3635 |
0.565 |
|
| 2012 |
Il Lee K, McLaughlin SG, Im W, Pastor RW. Langevin Dynamics Simulations of Protein Fencing of PIP2 Biophysical Journal. 102: 624a. DOI: 10.1016/J.Bpj.2011.11.3399 |
0.456 |
|
| 2012 |
Sun Lee H, Jo S, Im W. Absolute Binding Free Energy Calculations to Improve the Accuracy of Near-Native Ligand Pose Predictions Biophysical Journal. 102: 620a. DOI: 10.1016/J.Bpj.2011.11.3379 |
0.615 |
|
| 2012 |
Beaven AH, Kim T, Morris P, Anderson OS, Im W. Exploring Hydrophobic Mismatch's Impacts on Dissociation of Gramicidin a Channels using Molecular Dynamics Free Energy Simulations Biophysical Journal. 102: 496a. DOI: 10.1016/J.Bpj.2011.11.2717 |
0.527 |
|
| 2012 |
Wu L, Cheng X, Im W. A Structural Recognition Mechanism Study of MARCH and its Substrate Biophysical Journal. 102: 473a. DOI: 10.1016/J.Bpj.2011.11.2593 |
0.464 |
|
| 2012 |
Park S, Kim T, Im W. Window Exchange Umbrella Sampling Molecular Dynamics Simulations for Transmembrane Helix Assembly Biophysical Journal. 102: 398a. DOI: 10.1016/J.Bpj.2011.11.2174 |
0.614 |
|
| 2012 |
Il Lee K, Kim T, Pastor RW, Andersen OS, Im W. Assessment of Membrane Deformation Continuum Elastic Models Based on Molecular Simulations of Gramicidin A Biophysical Journal. 102: 296a. DOI: 10.1016/J.Bpj.2011.11.1637 |
0.591 |
|
| 2011 |
Jo S, Song KC, Desaire H, MacKerell AD, Im W. Glycan Reader: automated sugar identification and simulation preparation for carbohydrates and glycoproteins. Journal of Computational Chemistry. 32: 3135-41. PMID 21815173 DOI: 10.1002/Jcc.21886 |
0.779 |
|
| 2011 |
Rui H, Kumar R, Im W. Membrane tension, lipid adaptation, conformational changes, and energetics in MscL gating. Biophysical Journal. 101: 671-9. PMID 21806935 DOI: 10.1016/J.Bpj.2011.06.029 |
0.587 |
|
| 2011 |
Golebiewska U, Kay JG, Masters T, Grinstein S, Im W, Pastor RW, Scarlata S, McLaughlin S. Evidence for a fence that impedes the diffusion of phosphatidylinositol 4,5-bisphosphate out of the forming phagosomes of macrophages. Molecular Biology of the Cell. 22: 3498-507. PMID 21795401 DOI: 10.1091/Mbc.E11-02-0114 |
0.317 |
|
| 2011 |
Park H, Im W, Seok C. Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies. Biophysical Journal. 100: 2955-63. PMID 21689529 DOI: 10.1016/J.Bpj.2011.05.030 |
0.438 |
|
| 2011 |
Kim T, Jo S, Im W. Solid-state NMR ensemble dynamics as a mediator between experiment and simulation. Biophysical Journal. 100: 2922-8. PMID 21689525 DOI: 10.1016/J.Bpj.2011.02.063 |
0.731 |
|
| 2011 |
Jo S, Im W. Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables. Biophysical Journal. 100: 2913-21. PMID 21689524 DOI: 10.1016/J.Bpj.2011.05.009 |
0.663 |
|
| 2011 |
Song KC, Livanec PW, Klauda JB, Kuczera K, Dunn RC, Im W. Orientation of fluorescent lipid analogue BODIPY-PC to probe lipid membrane properties: insights from molecular dynamics simulations. The Journal of Physical Chemistry. B. 115: 6157-65. PMID 21513278 DOI: 10.1021/Jp109629V |
0.713 |
|
| 2011 |
Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophysical Journal. 100: 611-9. PMID 21281575 DOI: 10.1016/J.Bpj.2010.12.3708 |
0.591 |
|
| 2011 |
Rui H, Lee KI, Pastor RW, Im W. Molecular dynamics studies of ion permeation in VDAC. Biophysical Journal. 100: 602-10. PMID 21281574 DOI: 10.1016/J.Bpj.2010.12.3711 |
0.576 |
|
| 2011 |
Lee JH, Zhang Q, Jo S, Chai SC, Oh M, Im W, Lu H, Lim HS. Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions. Journal of the American Chemical Society. 133: 676-9. PMID 21171592 DOI: 10.1021/Ja108230S |
0.577 |
|
| 2011 |
Morris PM, Andersen OS, Im W. Exploring Hydrophobic Mismatch using Molecular Dynamics Simulations of Gramicidin A in Lipid Bilayers Biophysical Journal. 100: 501a. DOI: 10.1016/J.Bpj.2010.12.2933 |
0.499 |
|
| 2011 |
Rowland M, Pastor R, Im W. Computational Characterization of DMPI and DMPI(4)P Head Groups Biophysical Journal. 100: 493a. DOI: 10.1016/J.Bpj.2010.12.2889 |
0.496 |
|
| 2011 |
Song KC, Venable RM, Im W, Pastor RW. Molecular Dynamics Simulation Studies of Cardiolipin Bilayers Biophysical Journal. 100: 333a. DOI: 10.1016/J.Bpj.2010.12.2020 |
0.652 |
|
| 2011 |
Stuhlsatz D, Venable R, Im W. Properties of Lipid a Bilayers Analyzed by Molecular Dynamics Simulations Biophysical Journal. 100: 321a. DOI: 10.1016/J.Bpj.2010.12.1952 |
0.462 |
|
| 2011 |
Lee KI, Jo S, Rui H, Im W. Web-Based Interface for Brownian Dynamics Simulation of Ion Channels and Its Application to Vdac Biophysical Journal. 100: 156a. DOI: 10.1016/J.Bpj.2010.12.1068 |
0.711 |
|
| 2011 |
Jo S, Song K, MacKerell AD, Im W. First Step Towards Glycan Modeling: Charmm-Gui Glycan Reader and Glycan Database Biophysical Journal. 100: 156a. DOI: 10.1016/J.Bpj.2010.12.1066 |
0.757 |
|
| 2010 |
Jo S, Rui H, Lim JB, Klauda JB, Im W. Cholesterol flip-flop: insights from free energy simulation studies. The Journal of Physical Chemistry. B. 114: 13342-8. PMID 20923227 DOI: 10.1021/Jp108166K |
0.701 |
|
| 2010 |
Kim T, Im W. Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. Biophysical Journal. 99: 175-83. PMID 20655845 DOI: 10.1016/J.Bpj.2010.04.015 |
0.592 |
|
| 2010 |
Rui H, Im W. Protegrin-1 orientation and physicochemical properties in membrane bilayers studied by potential of mean force calculations. Journal of Computational Chemistry. 31: 2859-67. PMID 20589740 DOI: 10.1002/Jcc.21580 |
0.634 |
|
| 2010 |
Jepkorir G, RodrÃguez JC, Rui H, Im W, Lovell S, Battaile KP, Alontaga AY, Yukl ET, Moënne-Loccoz P, Rivera M. Structural, NMR spectroscopic, and computational investigation of hemin loading in the hemophore HasAp from Pseudomonas aeruginosa. Journal of the American Chemical Society. 132: 9857-72. PMID 20572666 DOI: 10.1021/Ja103498Z |
0.597 |
|
| 2010 |
Rathinavelan T, Zhang L, Picking WL, Weis DD, De Guzman RN, Im W. A repulsive electrostatic mechanism for protein export through the type III secretion apparatus. Biophysical Journal. 98: 452-61. PMID 20141759 DOI: 10.1016/J.Bpj.2009.10.030 |
0.382 |
|
| 2010 |
Song KC, Livanec PW, Dunn RC, Im W. Comparison of Lipid Monolayers and Bilayers by Comparative Molecular Dynamics Simulations of a Lipid-Like Dye Molecule Biophysical Journal. 98: 666a. DOI: 10.1016/J.Bpj.2009.12.4265 |
0.694 |
|
| 2010 |
Morris PM, Stuhlsatz D, Song K, Im W. Probing Cholesterol Dependent Lipid Properties Using Molecular Dynamics Simulations of BODIPY-PC in Explicit DMPC and DPPC Membranes Biophysical Journal. 98: 664a. DOI: 10.1016/J.Bpj.2009.12.4252 |
0.699 |
|
| 2010 |
Im W, McLaughlin S, Pastor RW. Hard to Fence You in: Computational Approaches to Explore the Hypothesis that Actin Filaments Impede PIP2 Diffusion in Membranes Biophysical Journal. 98: 688a. DOI: 10.1016/J.Bpj.2009.12.3778 |
0.352 |
|
| 2010 |
Golebiewska UP, Kay J, Grinstein S, Im W, Pastor R, Scarlata S, McLaughlin S. Don’t Fence Me in: Evidence for a ‘fence’ that Impedes the Diffusion of PIP2 Into and Out of Nascent Phagosomes in Macrophages Biophysical Journal. 98: 688a. DOI: 10.1016/J.Bpj.2009.12.3777 |
0.328 |
|
| 2010 |
Jo S, Im W. Transmembrane Helix Orientation and Dynamics Examined by Ensemble Dynamics with Solid-State NMR Observables and Potential of Mean Force Calculations Biophysical Journal. 98: 644a. DOI: 10.1016/J.Bpj.2009.12.3531 |
0.678 |
|
| 2010 |
Kim T, Im W. Revisiting Hydrophobic Mismatch with Free Energy Calculations of Transmembrane Helix Tilting Biophysical Journal. 98: 643a. DOI: 10.1016/J.Bpj.2009.12.3526 |
0.539 |
|
| 2010 |
Jo S, Im W. CHARMM-GUI: Brining Advanced Computational Techniques to Web Interface Biophysical Journal. 98: 568a. DOI: 10.1016/J.Bpj.2009.12.3078 |
0.631 |
|
| 2010 |
Kumar R, Rizk SS, Kossiakoff AA, Im W. Molecular Modeling and Simulations of the Transmembrane Domain of Human Growth Hormone Receptor Biophysical Journal. 98: 417a. DOI: 10.1016/J.Bpj.2009.12.2254 |
0.433 |
|
| 2010 |
Rui H, Im W. Protegrin-1 Orientation in Membrane Bilayers: Insights from Potential of Mean Force Calculations as A Function of Its Tilt and Rotation Angles Biophysical Journal. 98: 218a. DOI: 10.1016/J.Bpj.2009.12.1177 |
0.624 |
|
| 2009 |
Rui H, Lee J, Im W. Comparative molecular dynamics simulation studies of protegrin-1 monomer and dimer in two different lipid bilayers. Biophysical Journal. 97: 787-95. PMID 19651037 DOI: 10.1016/J.Bpj.2009.05.029 |
0.669 |
|
| 2009 |
Jo S, Lim JB, Klauda JB, Im W. CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophysical Journal. 97: 50-8. PMID 19580743 DOI: 10.1016/J.Bpj.2009.04.013 |
0.651 |
|
| 2009 |
Im W, Lee J, Kim T, Rui H. Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function. Journal of Computational Chemistry. 30: 1622-33. PMID 19496166 DOI: 10.1002/Jcc.21320 |
0.675 |
|
| 2009 |
Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, ... ... Im W, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287 |
0.635 |
|
| 2009 |
Kim T, Lee J, Im W. Molecular dynamics studies on structure and dynamics of phospholamban monomer and pentamer in membranes. Proteins. 76: 86-98. PMID 19089978 DOI: 10.1002/Prot.22322 |
0.615 |
|
| 2009 |
Lee J, Ham S, Im W. Beta-hairpin restraint potentials for calculations of potentials of mean force as a function of beta-hairpin tilt, rotation, and distance. Journal of Computational Chemistry. 30: 1334-43. PMID 19009593 DOI: 10.1002/Jcc.21154 |
0.36 |
|
| 2009 |
Rui H, Lee J, Im W. PG-1 Orientation in Lipid Bilayers: Insights from Molecular Dynamics Simulations and Calculations of Potentials of Mean Force as a Function of Its Tilt Angle Biophysical Journal. 96: 153a. DOI: 10.1016/J.Bpj.2008.12.693 |
0.653 |
|
| 2009 |
Kumar R, Im W. Computational Study of Transmembrane Domain of Cytokine Receptor Family Biophysical Journal. 96: 340a. DOI: 10.1016/J.Bpj.2008.12.3831 |
0.401 |
|
| 2009 |
Kim T, Im W. Investigation of Signal Transduction through the HAMP Domain from Molecular Dynamics Simulations Biophysical Journal. 96: 673a-674a. DOI: 10.1016/J.Bpj.2008.12.3560 |
0.51 |
|
| 2009 |
Rathinavelan T, Picking W, Guzman RDN, Im W. A Repulsive Electrostatic Mechanism For Protein Translocation Through Type III Secretion System: Insights From Pulling Simulations Of MxiH Across The Needle Apparatus Of Shigella Flexneri Biophysical Journal. 96: 78a. DOI: 10.1016/J.Bpj.2008.12.301 |
0.408 |
|
| 2009 |
Jo S, Lee J, Rathinavelan T, Im W. Ensemble Dynamics with Orientational NMR Restraints in Solution and Membrane Environments Biophysical Journal. 96: 65a. DOI: 10.1016/J.Bpj.2008.12.237 |
0.643 |
|
| 2009 |
Im W. Mechanisms and Energetics of Protein/Peptide Interactions in Biological Membranes Biophysical Journal. 96: 430a. DOI: 10.1016/J.Bpj.2008.12.2204 |
0.455 |
|
| 2008 |
Jo S, Vargyas M, Vasko-Szedlar J, Roux B, Im W. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucleic Acids Research. 36: W270-5. PMID 18508808 DOI: 10.1093/Nar/Gkn314 |
0.67 |
|
| 2008 |
Lee J, Chen J, Brooks CL, Im W. Application of solid-state NMR restraint potentials in membrane protein modeling. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 193: 68-76. PMID 18462966 DOI: 10.1016/J.Jmr.2008.04.023 |
0.437 |
|
| 2008 |
Lee J, Im W. Role of hydrogen bonding and helix-lipid interactions in transmembrane helix association. Journal of the American Chemical Society. 130: 6456-62. PMID 18422318 DOI: 10.1021/Ja711239H |
0.407 |
|
| 2008 |
Jo S, Kim T, Iyer VG, Im W. CHARMM-GUI: a web-based graphical user interface for CHARMM. Journal of Computational Chemistry. 29: 1859-65. PMID 18351591 DOI: 10.1002/Jcc.20945 |
0.661 |
|
| 2008 |
Rathinavelan T, Im W. A novel strategy to determine protein structures using exclusively residual dipolar coupling. Journal of Computational Chemistry. 29: 1640-9. PMID 18293296 DOI: 10.1002/Jcc.20923 |
0.386 |
|
| 2008 |
Lee J, Im W. Transmembrane helix tilting: insights from calculating the potential of mean force. Physical Review Letters. 100: 018103. PMID 18232823 DOI: 10.1103/Physrevlett.100.018103 |
0.408 |
|
| 2007 |
Jo S, Kim T, Im W. Automated builder and database of protein/membrane complexes for molecular dynamics simulations. Plos One. 2: e880. PMID 17849009 DOI: 10.1371/Journal.Pone.0000880 |
0.721 |
|
| 2007 |
Wang Y, Ouellette AN, Egan CW, Rathinavelan T, Im W, De Guzman RN. Differences in the electrostatic surfaces of the type III secretion needle proteins PrgI, BsaL, and MxiH. Journal of Molecular Biology. 371: 1304-14. PMID 17617421 DOI: 10.1016/J.Jmb.2007.06.034 |
0.349 |
|
| 2007 |
Rathinavelan T, Im W. Explicit treatment of force contribution from alignment tensor using overdetermined linear equations and its application in NMR structure determination. Journal of Computational Chemistry. 28: 1858-64. PMID 17405113 DOI: 10.1002/Jcc.20712 |
0.383 |
|
| 2007 |
Lee J, Im W. Implementation and application of helix-helix distance and crossing angle restraint potentials. Journal of Computational Chemistry. 28: 669-80. PMID 17195157 DOI: 10.1002/Jcc.20614 |
0.398 |
|
| 2007 |
Bu L, Im W, Brooks CL. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophysical Journal. 92: 854-63. PMID 17085501 DOI: 10.1529/Biophysj.106.095216 |
0.433 |
|
| 2007 |
Lee J, Im W. Restraint potential and free energy decomposition formalism for helical tilting Chemical Physics Letters. 441: 132-135. DOI: 10.1016/J.Cplett.2007.05.003 |
0.359 |
|
| 2006 |
Liu Y, Scolari M, Im W, Woo HJ. Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: a molecular dynamics study. Proteins. 64: 156-66. PMID 16645962 DOI: 10.1002/Prot.20993 |
0.382 |
|
| 2006 |
Chen J, Im W, Brooks CL. Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. Journal of the American Chemical Society. 128: 3728-36. PMID 16536547 DOI: 10.1021/Ja057216R |
0.413 |
|
| 2005 |
Im W, Chen J, Brooks CL. Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Advances in Protein Chemistry. 72: 173-98. PMID 16581377 DOI: 10.1016/S0065-3233(05)72007-6 |
0.328 |
|
| 2005 |
Chen J, Im W, Brooks CL. Application of torsion angle molecular dynamics for efficient sampling of protein conformations. Journal of Computational Chemistry. 26: 1565-78. PMID 16145655 DOI: 10.1002/Jcc.20293 |
0.427 |
|
| 2005 |
Im W, Brooks CL. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 102: 6771-6. PMID 15860587 DOI: 10.1073/Pnas.0408135102 |
0.454 |
|
| 2005 |
Chen J, Won HS, Im W, Dyson HJ, Brooks CL. Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. Journal of Biomolecular Nmr. 31: 59-64. PMID 15692739 DOI: 10.1007/S10858-004-6056-Z |
0.385 |
|
| 2004 |
Roux B, Allen T, Bernèche S, Im W. Theoretical and computational models of biological ion channels. Quarterly Reviews of Biophysics. 37: 15-103. PMID 17390604 DOI: 10.1017/S0033583504003968 |
0.649 |
|
| 2004 |
Chen J, Im W, Brooks CL. Refinement of NMR structures using implicit solvent and advanced sampling techniques. Journal of the American Chemical Society. 126: 16038-47. PMID 15584737 DOI: 10.1021/Ja047624F |
0.383 |
|
| 2004 |
Noskov SY, Im W, Roux B. Ion permeation through the alpha-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophysical Journal. 87: 2299-309. PMID 15454431 DOI: 10.1529/Biophysj.104.044008 |
0.644 |
|
| 2004 |
Feig M, Im W, Brooks CL. Implicit solvation based on generalized Born theory in different dielectric environments. The Journal of Chemical Physics. 120: 903-11. PMID 15267926 DOI: 10.1063/1.1631258 |
0.308 |
|
| 2004 |
Im W, Brooks CL. De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. Journal of Molecular Biology. 337: 513-9. PMID 15019773 DOI: 10.1016/J.Jmb.2004.01.045 |
0.5 |
|
| 2004 |
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. Journal of Computational Chemistry. 25: 265-84. PMID 14648625 DOI: 10.1002/Jcc.10378 |
0.388 |
|
| 2003 |
Im W, Feig M, Brooks CL. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophysical Journal. 85: 2900-18. PMID 14581194 DOI: 10.1016/S0006-3495(03)74712-2 |
0.462 |
|
| 2003 |
Im W, Lee MS, Brooks CL. Generalized born model with a simple smoothing function. Journal of Computational Chemistry. 24: 1691-702. PMID 12964188 DOI: 10.1002/Jcc.10321 |
0.315 |
|
| 2002 |
Im W, Roux B. Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. Journal of Molecular Biology. 322: 851-69. PMID 12270719 DOI: 10.1016/S0022-2836(02)00778-7 |
0.494 |
|
| 2002 |
Im W, Roux B. 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. Journal of Molecular Biology. 319: 1177-97. PMID 12079356 DOI: 10.1016/S0022-2836(02)00380-7 |
0.535 |
|
| 2002 |
Philippsen A, Im W, Engel A, Schirmer T, Roux B, Müller DJ. Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophysical Journal. 82: 1667-76. PMID 11867478 DOI: 10.1016/S0006-3495(02)75517-3 |
0.523 |
|
| 2002 |
Banavali NK, Im W, Roux B. Electrostatic free energy calculations using the generalized solvent boundary potential method The Journal of Chemical Physics. 117: 7381-7388. DOI: 10.1063/1.1507108 |
0.518 |
|
| 2001 |
Im W, Roux B. Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry The Journal of Chemical Physics. 115: 4850-4861. DOI: 10.1063/1.1390507 |
0.54 |
|
| 2001 |
Im W, Bernèche S, Roux B. Generalized solvent boundary potential for computer simulations The Journal of Chemical Physics. 114: 2924-2937. DOI: 10.1063/1.1336570 |
0.482 |
|
| 2000 |
Roux B, Bernèche S, Im W. Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry. 39: 13295-306. PMID 11063565 DOI: 10.1021/Bi001567V |
0.437 |
|
| 2000 |
Im W, Seefeld S, Roux B. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophysical Journal. 79: 788-801. PMID 10920012 DOI: 10.1016/S0006-3495(00)76336-3 |
0.524 |
|
| 1999 |
Nina M, Im W, Roux B. Optimized atomic radii for protein continuum electrostatics solvation forces. Biophysical Chemistry. 78: 89-96. PMID 17030305 DOI: 10.1016/S0301-4622(98)00236-1 |
0.494 |
|
| 1998 |
Im W, Beglov D, Roux B. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Computer Physics Communications. 111: 59-75. DOI: 10.1016/S0010-4655(98)00016-2 |
0.469 |
|
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