| CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field J Lee, X Cheng, JM Swails, MS Yeom, PK Eastman, JA Lemkul, S Wei, ... Journal of chemical theory and computation 12 (1), 405-413, 2016 | 3581 | 2016 |
| CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations EL Wu, X Cheng, S Jo, H Rui, KC Song, EM Dávila‐Contreras, Y Qi, J Lee, ... Journal of computational chemistry 35 (27), 1997-2004, 2014 | 2318 | 2014 |
| CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans J Lee, DS Patel, J Ståhle, SJ Park, NR Kern, S Kim, J Lee, X Cheng, ... Journal of chemical theory and computation 15 (1), 775-786, 2018 | 531 | 2018 |
| CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules S Kim, J Lee, S Jo, CL Brooks III, HS Lee, W Im Journal of computational chemistry 38 (21), 1879-1886, 2017 | 472 | 2017 |
| CHARMM-GUI Martini maker for coarse-grained simulations with the Martini force field Y Qi, HI Ingólfsson, X Cheng, J Lee, SJ Marrink, W Im Journal of chemical theory and computation 11 (9), 4486-4494, 2015 | 450 | 2015 |
| CHARMM‐GUI 10 years for biomolecular modeling and simulation S Jo, X Cheng, J Lee, S Kim, SJ Park, DS Patel, AH Beaven, KI Lee, H Rui, ... Journal of computational chemistry 38 (15), 1114-1124, 2017 | 313 | 2017 |
| CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates SJ Park, J Lee, Y Qi, NR Kern, HS Lee, S Jo, IS Joung, K Joo, J Lee, W Im Glycobiology 29 (4), 320-331, 2019 | 309 | 2019 |
| CHARMM-GUI supports the Amber force fields J Lee, M Hitzenberger, M Rieger, NR Kern, M Zacharias, W Im The Journal of Chemical Physics 153 (3), 035103, 2020 | 278 | 2020 |
| Developing a fully glycosylated full-length SARS-CoV-2 spike protein model in a viral membrane H Woo, SJ Park, YK Choi, T Park, M Tanveer, Y Cao, NR Kern, J Lee, ... The Journal of Physical Chemistry B 124 (33), 7128-7137, 2020 | 250 | 2020 |
| CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides PC Hsu, BMH Bruininks, D Jefferies, P Cesar Telles de Souza, J Lee, ... Journal of Computational Chemistry 38 (27), 2354-2363, 2017 | 193 | 2017 |
| Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank SJ Park, J Lee, DS Patel, H Ma, HS Lee, S Jo, W Im Bioinformatics 33 (19), 3051-3057, 2017 | 127 | 2017 |
| CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems YK Choi, NR Kern, S Kim, K Kanhaiya, Y Afshar, SH Jeon, S Jo, ... Journal of chemical theory and computation 18 (1), 479-493, 2021 | 123 | 2021 |
| CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers YK Choi, SJ Park, S Park, S Kim, NR Kern, J Lee, W Im Journal of chemical theory and computation 17 (4), 2431-2443, 2021 | 112 | 2021 |
| CHARMM-GUI HMMM builder for membrane simulations with the highly mobile membrane-mimetic model Y Qi, X Cheng, J Lee, JV Vermaas, TV Pogorelov, E Tajkhorshid, S Park, ... Biophysical journal 109 (10), 2012-2022, 2015 | 108 | 2015 |
| CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides Y Gao, J Lee, IPS Smith, H Lee, S Kim, Y Qi, JB Klauda, G Widmalm, ... Journal of chemical information and modeling 61 (2), 831-839, 2021 | 101 | 2021 |
| CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations S Kim, H Oshima, H Zhang, NR Kern, S Re, J Lee, B Roux, Y Sugita, ... Journal of chemical theory and computation 16 (11), 7207-7218, 2020 | 86 | 2020 |
| Additive CHARMM36 Force Field for Nonstandard Amino Acids A Croitoru, SJ Park, A Kumar, J Lee, W Im, AD MacKerell Jr, ... Journal of Chemical Theory and Computation, 2021 | 77 | 2021 |
| CHARMM-GUI PDB manipulator: various PDB structural modifications for biomolecular modeling and simulation SJ Park, N Kern, T Brown, J Lee, W Im Journal of Molecular Biology, 167995, 2023 | 71 | 2023 |
| CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids S Park, YK Choi, S Kim, J Lee, W Im Journal of chemical information and modeling 61 (10), 5192-5202, 2021 | 67 | 2021 |
| Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes ID Pogozheva, GA Armstrong, L Kong, TJ Hartnagel, CA Carpino, SE Gee, ... Journal of Chemical Information and Modeling, 2022 | 63 | 2022 |