| Year |
Citation |
Score |
| 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 |
0.499 |
|
| 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 |
0.59 |
|
| 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 |
0.552 |
|
| 2019 |
Suh D, Jo S, Jiang W, Chipot C, Roux B. String method for Protein-Protein Binding Free Energy Calculations. Journal of Chemical Theory and Computation. PMID 31593627 DOI: 10.1021/Acs.Jctc.9B00499 |
0.524 |
|
| 2019 |
Ustach VD, Lakkaraju SKK, Jo S, Yu W, Jiang W, MacKerell AD. Optimization and Evaluation of the Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. Journal of Chemical Information and Modeling. PMID 31034213 DOI: 10.1021/Acs.Jcim.9B00210 |
0.352 |
|
| 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 |
0.601 |
|
| 2018 |
Yu W, Jo S, Lakkaraju SK, Weber DJ, MacKerell AD. Exploring protein-protein interactions using the Site-Identification by Ligand Competitive Saturation (SILCS) methodology. Proteins. PMID 30582220 DOI: 10.1002/Prot.25650 |
0.387 |
|
| 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, 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 |
0.593 |
|
| 2018 |
Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 30480445 DOI: 10.1021/Acs.Jctc.8B01075 |
0.534 |
|
| 2018 |
Jiang W, Thirman J, Jo S, Roux B. Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis. The Journal of Physical Chemistry. B. PMID 30253098 DOI: 10.1021/Acs.Jpcb.8B03277 |
0.53 |
|
| 2018 |
Sun D, Lakkaraju SK, Jo S, MacKerell AD. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water. Journal of Chemical Theory and Computation. PMID 30183291 DOI: 10.1021/Acs.Jctc.8B00604 |
0.435 |
|
| 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 |
0.573 |
|
| 2017 |
Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 29111720 DOI: 10.1021/Acs.Jctc.7B00875 |
0.549 |
|
| 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 |
0.504 |
|
| 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 |
0.563 |
|
| 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 |
0.561 |
|
| 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, et al. CHARMM-GUI 10 years for biomolecular modeling and simulation. Journal of Computational Chemistry. PMID 27862047 DOI: 10.1002/Jcc.24660 |
0.755 |
|
| 2016 |
Jo S, Suh D, He Z, Chipot C, Roux B. Leveraging the Information from Markov State Models to Improve the Convergence of Umbrella Sampling Simulations. The Journal of Physical Chemistry. B. PMID 27409349 DOI: 10.1021/Acs.Jpcb.6B05125 |
0.562 |
|
| 2016 |
Jiang W, Jo S. Accelerating Orthogonal Space Sampling with Replica Exchange with Solute Tempering (REST2) through a Generic Implementation in NAMD Biophysical Journal. 110: 641a-642a. DOI: 10.1016/J.Bpj.2015.11.3433 |
0.419 |
|
| 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, 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 |
0.601 |
|
| 2015 |
Jo S, Chipot C, Roux B. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics. Journal of Chemical Theory and Computation. 11: 2234-44. PMID 26574422 DOI: 10.1021/Ct501034W |
0.555 |
|
| 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 |
0.478 |
|
| 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 |
0.574 |
|
| 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 |
0.637 |
|
| 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 |
0.534 |
|
| 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 |
0.616 |
|
| 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 |
0.596 |
|
| 2015 |
Jo S, Chipot C, Roux B. Efficient determination of relative entropy using combined temperature and hamiltonian replica-exchange molecular dynamics Journal of Chemical Theory and Computation. 11: 2234-2244. DOI: 10.1021/ct501034w |
0.417 |
|
| 2015 |
Jo S, Jiang W. A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations Computer Physics Communications. 197: 304-311. DOI: 10.1016/J.Cpc.2015.08.030 |
0.384 |
|
| 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 |
0.611 |
|
| 2015 |
Pond MP, Jo S, Hyde HC, Wright MH, Blachowicz L, Bezanilla F, Roux B. Computational and Experimental Characterization of Intramolecular Regulatory Interactions in Hck Biophysical Journal. 108: 533a. DOI: 10.1016/J.Bpj.2014.11.2923 |
0.46 |
|
| 2015 |
Jo S, Jiang W, Roux B. Quantifying Protein-Protein Binding Energy and Entropy using Molecular Dynamics Simulations Biophysical Journal. 108: 41a. DOI: 10.1016/J.Bpj.2014.11.251 |
0.531 |
|
| 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 |
0.736 |
|
| 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 |
0.618 |
|
| 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 |
0.689 |
|
| 2014 |
Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. Plos Computational Biology. 10: e1003521. PMID 24699246 DOI: 10.1371/Journal.Pcbi.1003521 |
0.526 |
|
| 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 |
0.605 |
|
| 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 |
0.604 |
|
| 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 |
0.664 |
|
| 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 |
0.628 |
|
| 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 |
0.553 |
|
| 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 |
0.624 |
|
| 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 |
0.623 |
|
| 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 |
0.539 |
|
| 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 |
0.626 |
|
| 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 |
0.518 |
|
| 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 |
0.61 |
|
| 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 |
0.588 |
|
| 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 |
0.513 |
|
| 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 |
0.613 |
|
| 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 |
0.549 |
|
| 2012 |
Zhong D, Lefebre M, Kaur K, McDowell MA, Gdowski C, Jo S, Wang Y, Benedict SH, Lea SM, Galan JE, De Guzman RN. The Salmonella type III secretion system inner rod protein PrgJ is partially folded. The Journal of Biological Chemistry. 287: 25303-11. PMID 22654099 DOI: 10.1074/Jbc.M112.381574 |
0.365 |
|
| 2012 |
Kwon T, Roux B, Jo S, Klauda JB, Harris AL, Bargiello TA. Molecular dynamics simulations of the Cx26 hemichannel: insights into voltage-dependent loop-gating. Biophysical Journal. 102: 1341-51. PMID 22455917 DOI: 10.1016/J.Bpj.2012.02.009 |
0.492 |
|
| 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 |
0.714 |
|
| 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 |
0.685 |
|
| 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 |
0.557 |
|
| 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 |
0.57 |
|
| 2012 |
Stuhlsatz D, Im W, Jo S, Widmalm G. Molecular Dynamics Simulations of E. Coli Lipoplysacharide Bilayers Biophysical Journal. 102: 185a. DOI: 10.1016/J.Bpj.2011.11.1009 |
0.343 |
|
| 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 |
0.634 |
|
| 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 |
0.686 |
|
| 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 |
0.604 |
|
| 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 |
0.501 |
|
| 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 |
0.662 |
|
| 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 |
0.594 |
|
| 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 |
0.64 |
|
| 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 |
0.613 |
|
| 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 |
0.606 |
|
| 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 |
0.546 |
|
| 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 |
0.581 |
|
| 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 |
0.629 |
|
| 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 |
0.637 |
|
| 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 |
0.665 |
|
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