| 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 | 2850 | 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 | 1931 | 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 | 390 | 2018 |
| 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 | 385 | 2015 |
| Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study HS Lee, Y Qi, W Im Scientific reports 5 (1), 1-7, 2015 | 281 | 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, ... J Comput Chem., 2016 | 258 | 2016 |
| Chapter Eight-CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues S Jo, X Cheng, SM Islam, L Huang, H Rui, A Zhu, HS Lee, Y Qi, W Han, ... Advances in protein chemistry and structural biology 96, 235-265, 2014 | 239 | 2014 |
| 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 | 238 | 2019 |
| Computational protein design with deep learning neural networks J Wang, H Cao, JZH Zhang, Y Qi Scientific reports 8 (1), 1-9, 2018 | 224 | 2018 |
| DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks H Cao, J Wang, L He, Y Qi, JZ Zhang Journal of chemical information and modeling 59 (4), 1508-1514, 2019 | 172 | 2019 |
| CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides PC Hsu, BMH Bruininks, D Jefferies, PCT de Souza, J Lee, DS Patel, ... Journal of Computational Chemistry 38 (27), 2354–2363, 2017 | 161 | 2017 |
| LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro Q Li, X Peng, Y Li, W Tang, J Zhu, J Huang, Y Qi, Z Zhang Nucleic Acids Research 48 (D1), D320-D327, 2020 | 140 | 2020 |
| 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 | 98 | 2015 |
| Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability DS Patel, S Re, EL Wu, Y Qi, PE Klebba, G Widmalm, MS Yeom, Y Sugita, ... Biophysical journal 110 (4), 930-938, 2016 | 78 | 2016 |
| BamA POTRA Domain Interacts with a Native Lipid Membrane Surface PJ Fleming, DS Patel, EL Wu, Y Qi, MS Yeom, MC Sousa, KG Fleming, ... Biophysical Journal 110 (12), 2698-2709, 2016 | 73 | 2016 |
| DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet Y Qi, JZH Zhang Journal of Chemical Information and Modeling 60 (3), 1245-1252, 2020 | 69 | 2020 |
| 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 | 62 | 2021 |
| CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations Y Qi, X Cheng, W Han, S Jo, K Schulten, W Im Journal of Chemical Information and Modeling 54 (3), 1003–1009, 2014 | 59 | 2014 |
| Maturation mechanism of severe acute respiratory syndrome (SARS) coronavirus 3C-like proteinase C Li, Y Qi, X Teng, Z Yang, P Wei, C Zhang, L Tan, L Zhou, Y Liu, L Lai Journal of Biological Chemistry 285 (36), 28134-28140, 2010 | 57 | 2010 |
| Modeling and simulation of bacterial outer membranes and interactions with membrane proteins DS Patel, Y Qi, W Im Current Opinion in Structural Biology 43, 131-140, 2017 | 55 | 2017 |
Wonpil ImPresidential Endowed Chair and Professor of Biological Sciences, Lehigh UniversityVerified email at lehigh.edu
