| AMBER 2018 DA Case, TA Darden, RE Duke, D Ghoreishi, MK Gilson, H Gohlke, ... University of California, San Francisco, 2018 | 6026* | 2018 |
| Recent advances in implicit solvent-based methods for biomolecular simulations J Chen, CL Brooks III, J Khandogin Current opinion in structural biology 18 (2), 140-148, 2008 | 391 | 2008 |
| Constant pH molecular dynamics with proton tautomerism J Khandogin, CL Brooks Biophysical journal 89 (1), 141-157, 2005 | 331 | 2005 |
| Progress in the prediction of pKa values in proteins E Alexov, EL Mehler, N Baker, A M. Baptista, Y Huang, F Milletti, ... Proteins: structure, function, and bioinformatics 79 (12), 3260-3275, 2011 | 289 | 2011 |
| Continuous constant pH molecular dynamics in explicit solvent with pH-based replica exchange JA Wallace, JK Shen Journal of chemical theory and computation 7 (8), 2617-2629, 2011 | 230 | 2011 |
| Toward the accurate first-principles prediction of ionization equilibria in proteins J Khandogin, CL Brooks Biochemistry 45 (31), 9363-9373, 2006 | 193 | 2006 |
| Linking folding with aggregation in Alzheimer's β-amyloid peptides J Khandogin, CL Brooks III Proceedings of the National Academy of Sciences 104 (43), 16880-16885, 2007 | 181 | 2007 |
| All-atom continuous constant pH molecular dynamics with particle mesh Ewald and titratable water Y Huang, W Chen, JA Wallace, J Shen Journal of chemical theory and computation 12 (11), 5411-5421, 2016 | 123 | 2016 |
| Recent development and application of constant pH molecular dynamics W Chen, BH Morrow, C Shi, JK Shen Molecular simulation 40 (10-11), 830-838, 2014 | 122 | 2014 |
| pH-responsive self-assembly of polysaccharide through a rugged energy landscape BH Morrow, GF Payne, J Shen Journal of the American Chemical Society 137 (40), 13024-13030, 2015 | 113 | 2015 |
| Chitosan to connect biology to electronics: Fabricating the bio-device interface and communicating across this interface E Kim, Y Xiong, Y Cheng, HC Wu, Y Liu, BH Morrow, H Ben-Yoav, ... Polymers 7 (1), 1-46, 2014 | 112 | 2014 |
| Assessing lysine and cysteine reactivities for designing targeted covalent kinase inhibitors R Liu, Z Yue, CC Tsai, J Shen Journal of the American Chemical Society 141 (16), 6553-6560, 2019 | 110 | 2019 |
| Exploring atomistic details of pH-dependent peptide folding J Khandogin, J Chen, CL Brooks III Proceedings of the National Academy of Sciences 103 (49), 18546-18550, 2006 | 108 | 2006 |
| Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA Y Huang, W Chen, DL Dotson, O Beckstein, J Shen Nature communications 7 (1), 12940, 2016 | 105 | 2016 |
| Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH JA Wallace, JK Shen The Journal of Chemical Physics 137 (18), 2012 | 105 | 2012 |
| AMBER 2020 TA Darden, RE Duke, G Giambasu, MK Gilson, H Gohlke, AW Goetz, ... University of California: San Francisco, 2020 | 97* | 2020 |
| Predicting pKa values with continuous constant pH molecular dynamics JA Wallace, JK Shen Methods in enzymology 466, 455-475, 2009 | 95 | 2009 |
| How μ-opioid receptor recognizes fentanyl QN Vo, P Mahinthichaichan, J Shen, CR Ellis Nature communications 12 (1), 984, 2021 | 91 | 2021 |
| Introducing titratable water to all-atom molecular dynamics at constant pH W Chen, JA Wallace, Z Yue, JK Shen Biophysical journal 105 (4), L15-L17, 2013 | 87 | 2013 |
| pH-dependent population shift regulates BACE1 activity and inhibition CR Ellis, J Shen Journal of the American Chemical Society 137 (30), 9543-9546, 2015 | 82 | 2015 |
Gregory PayneProfessor, University of MarylandVerified email at umd.edu
