| Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field D Shivakumar, J Williams, Y Wu, W Damm, J Shelley, W Sherman Journal of chemical theory and computation 6 (5), 1509-1519, 2010 | 1630 | 2010 |
| Flexible simple point-charge water model with improved liquid-state properties Y Wu, HL Tepper, GA Voth The Journal of chemical physics 124 (2), 024503, 2006 | 1288 | 2006 |
| Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field L Wang, Y Wu, Y Deng, B Kim, L Pierce, G Krilov, D Lupyan, S Robinson, ... Journal of the American Chemical Society 137 (7), 2695-2703, 2015 | 1097 | 2015 |
| Proton solvation and transport in aqueous and biomolecular systems: Insights from computer simulations JMJ Swanson, CM Maupin, H Chen, MK Petersen, J Xu, Y Wu, GA Voth The Journal of Physical Chemistry B 111 (17), 4300-4314, 2007 | 324 | 2007 |
| An improved multistate empirical valence bond model for aqueous proton solvation and transport Y Wu, H Chen, F Wang, F Paesani, GA Voth The Journal of Physical Chemistry B 112 (2), 467-482, 2008 | 288 | 2008 |
| Modeling local structural rearrangements using FEP/REST: application to relative binding affinity predictions of CDK2 inhibitors L Wang, Y Deng, JL Knight, Y Wu, B Kim, W Sherman, JC Shelley, T Lin, ... Journal of chemical theory and computation 9 (2), 1282-1293, 2013 | 205 | 2013 |
| Proton transport behavior through the influenza A M2 channel: insights from molecular simulation H Chen, Y Wu, GA Voth Biophysical Journal 93 (10), 3470-3479, 2007 | 134 | 2007 |
| Lead optimization mapper: automating free energy calculations for lead optimization S Liu, Y Wu, T Lin, R Abel, JP Redmann, CM Summa, VR Jaber, NM Lim, ... Journal of computer-aided molecular design 27, 755-770, 2013 | 131 | 2013 |
| Accurate modeling of scaffold hopping transformations in drug discovery L Wang, Y Deng, Y Wu, B Kim, DN LeBard, D Wandschneider, M Beachy, ... Journal of chemical theory and computation 13 (1), 42-54, 2017 | 121 | 2017 |
| Accurate calculation of relative binding free energies between ligands with different net charges W Chen, Y Deng, E Russell, Y Wu, R Abel, L Wang Journal of chemical theory and computation 14 (12), 6346-6358, 2018 | 96 | 2018 |
| Charge delocalization in proton channels, I: the aquaporin channels and proton blockage H Chen, B Ilan, Y Wu, F Zhu, K Schulten, GA Voth Biophysical journal 92 (1), 46-60, 2007 | 94 | 2007 |
| Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel H Chen, Y Wu, GA Voth Biophysical journal 90 (10), L73-L75, 2006 | 90 | 2006 |
| A computer simulation study of the hydrated proton in a synthetic proton channel Y Wu, GA Voth Biophysical journal 85 (2), 864-875, 2003 | 70 | 2003 |
| A computational study of the closed and open states of the influenza a M2 proton channel Y Wu, GA Voth Biophysical journal 89 (4), 2402-2411, 2005 | 57 | 2005 |
| Accurate and reliable prediction of the binding affinities of macrocycles to their protein targets HS Yu, Y Deng, Y Wu, D Sindhikara, AR Rask, T Kimura, R Abel, L Wang Journal of chemical theory and computation 13 (12), 6290-6300, 2017 | 46 | 2017 |
| Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity Y Wu, B Ilan, GA Voth Biophysical journal 92 (1), 61-69, 2007 | 34 | 2007 |
| Computational studies of proton transport through the M2 channel Y Wu, GA Voth FEBS letters 552 (1), 23-27, 2003 | 34 | 2003 |
| Thermal stable and oxidation-resistant variant of subtilisin E Y Yang, L Jiang, L Zhu, Y Wu, S Yang Journal of biotechnology 81 (2-3), 113-118, 2000 | 32 | 2000 |
| Toward atomistic modeling of irreversible covalent inhibitor binding kinetics HS Yu, C Gao, D Lupyan, Y Wu, T Kimura, C Wu, L Jacobson, E Harder, ... Journal of chemical information and modeling 59 (9), 3955-3967, 2019 | 29 | 2019 |
| Harder, Woody Sherman, Mark Brewer, Ron Wester, Mark Murcko, Leah Frye, Ramy Farid, Teng Lin, David L. Mobley, William L. Jorgensen, Bruce J. Berne, Richard A. Friesner, and … L Wang, Y Wu, Y Deng, B Kim, L Pierce, G Krilov, D Lupyan, S Robinson, ... J. Am. Chem. Soc 137 (7), 2695-2703, 2015 | 28 | 2015 |
