Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity AL Kaplan, DN Confair, K Kim, X Barros-Álvarez, RM Rodriguiz, Y Yang, ... Nature 610 (7932), 582-591, 2022 | 143 | 2022 |
A PLCγ1-dependent, force-sensitive signaling network in the myogenic constriction of cerebral arteries AL Gonzales, Y Yang, MN Sullivan, L Sanders, F Dabertrand, ... Science signaling 7 (327), ra49-ra49, 2014 | 126 | 2014 |
Efficient exploration of chemical space with docking and deep learning Y Yang, K Yao, MP Repasky, K Leswing, R Abel, BK Shoichet, SV Jerome Journal of Chemical Theory and Computation 17 (11), 7106-7119, 2021 | 124 | 2021 |
Property-unmatched decoys in docking benchmarks RM Stein, Y Yang, TE Balius, MJ O’Meara, J Lyu, J Young, K Tang, ... Journal of chemical information and modeling 61 (2), 699-714, 2021 | 74 | 2021 |
Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning AH Mahmoud, MR Masters, Y Yang, MA Lill Communications Chemistry 3 (1), 19, 2020 | 59 | 2020 |
Ligand strain energy in large library docking S Gu, MS Smith, Y Yang, JJ Irwin, BK Shoichet Journal of chemical information and modeling 61 (9), 4331-4341, 2021 | 35 | 2021 |
Ranking protein–protein docking results using steered molecular dynamics and potential of mean force calculations LJ Kingsley, J Esquivel‐Rodríguez, Y Yang, D Kihara, MA Lill Journal of computational chemistry 37 (20), 1861-1865, 2016 | 29 | 2016 |
Analysis of factors influencing hydration site prediction based on molecular dynamics simulations Y Yang, B Hu, MA Lill Journal of Chemical Information and Modeling 54 (10), 2987-2995, 2014 | 25 | 2014 |
Efficient and accurate hydration site profiling for enclosed binding sites MR Masters, AH Mahmoud, Y Yang, MA Lill Journal of chemical information and modeling 58 (11), 2183-2188, 2018 | 22 | 2018 |
Inactive and active state structures template selective tools for the human 5-HT5A receptor S Zhang, H Chen, C Zhang, Y Yang, P Popov, J Liu, BE Krumm, C Cao, ... Nature structural & molecular biology 29 (7), 677-687, 2022 | 19 | 2022 |
WATsite2. 0 with PyMOL Plugin: Hydration site prediction and visualization Y Yang, B Hu, MA Lill Protein Function Prediction: Methods and Protocols, 123-134, 2017 | 18 | 2017 |
Modeling of halogen–protein interactions in co-solvent molecular dynamics simulations Y Yang, AH Mahmoud, MA Lill Journal of chemical information and modeling 59 (1), 38-42, 2018 | 11 | 2018 |
Dissecting the influence of protein flexibility on the location and thermodynamic profile of explicit water molecules in protein–ligand binding Y Yang, MA Lill Journal of chemical theory and computation 12 (9), 4578-4592, 2016 | 9 | 2016 |
Improving Atom-Type Diversity and Sampling in Cosolvent Simulations Using λ-Dynamics AH Mahmoud, Y Yang, MA Lill Journal of chemical theory and computation 15 (5), 3272-3287, 2019 | 8 | 2019 |
Calculation of thermodynamic properties of bound water molecules Y Yang, AHA Abdallah, MA Lill Computational Drug Discovery and Design, 389-402, 2018 | 7 | 2018 |
Membrane Stretch‐Induced Activation of TRPM4 in Cerebral Artery Smooth Muscle Cells Y Yang, AL Gonzales, L Sanders, S Earley The FASEB Journal 26, 685.35-685.35, 2012 | 3 | 2012 |
High-throughput hydrogen bond strength calculation and its applications in optimizing drug ADME properties J Shen, Y Yang, H Broughton, IA Watson, PV Desai Future Medicinal Chemistry 11 (6), 511-524, 2019 | 2 | 2019 |
Computational Modeling of (De)-Solvation Effects and Protein Flexibility in Protein-Ligand Binding Using Molecular Dynamics Simulations Y Yang Purdue University, 2018 | | 2018 |
Influence of protein flexibility on ligand pathway prediction and hydration site identification MA Lill, LJ Kingsley, Y Yang EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 44, S148-S148, 2015 | | 2015 |
WATsite. User Guide A GPU-accelerated Hydration Site Prediction Program with PyMOL Plugin Y Yang, MR Masters, AH Mahmoud, B Hu, MA Lill | | |