| Polarizable atomic multipole-based AMOEBA force field for proteins Y Shi, Z Xia, J Zhang, R Best, C Wu, JW Ponder, P Ren Journal of chemical theory and computation 9 (9), 4046-4063, 2013 | 715 | 2013 |
| The structure, thermodynamics, and solubility of organic crystals from simulation with a polarizable force field MJ Schnieders, J Baltrusaitis, Y Shi, G Chattree, L Zheng, W Yang, P Ren Journal of Chemical Theory and Computation 8 (5), 1721-1736, 2012 | 95 | 2012 |
| RNA 3D structure prediction by using a coarse-grained model and experimental data Z Xia, DR Bell, Y Shi, P Ren The Journal of Physical Chemistry B 117 (11), 3135-3144, 2013 | 91 | 2013 |
| Multipole electrostatics in hydration free energy calculations Y Shi, C Wu, JW Ponder, P Ren Journal of computational chemistry 32 (5), 967-977, 2011 | 82 | 2011 |
| Polarizable force fields for biomolecular modeling Y Shi, P Ren, M Schnieders, JP Piquemal Reviews in Computational Chemistry Volume 28, 51-86, 2015 | 62 | 2015 |
| Probing the effect of conformational constraint on phosphorylated ligand binding to an SH2 domain using polarizable force field simulations Y Shi, CZ Zhu, SF Martin, P Ren The Journal of Physical Chemistry B 116 (5), 1716-1727, 2012 | 56 | 2012 |
| Molecular docking simulations for macromolecularly imprinted polymers DR Kryscio, Y Shi, P Ren, NA Peppas Industrial & engineering chemistry research 50 (24), 13877-13884, 2011 | 38 | 2011 |
| From in silico discovery to intracellular activity: targeting JNK–protein interactions with small molecules TS Kaoud, C Yan, S Mitra, CC Tseng, J Jose, JM Taliaferro, ... ACS medicinal chemistry letters 3 (9), 721-725, 2012 | 30 | 2012 |
| Reversible covalent inhibition of eEF‐2K by carbonitriles AK Devkota, R Edupuganti, C Yan, Y Shi, J Jose, Q Wang, TS Kaoud, ... ChemBioChem 15 (16), 2435-2442, 2014 | 27 | 2014 |
| Manipulating JNK signaling with (−)-zuonin A TS Kaoud, H Park, S Mitra, C Yan, CC Tseng, Y Shi, J Jose, JM Taliaferro, ... ACS chemical biology 7 (11), 1873-1883, 2012 | 24 | 2012 |
| Trypsin-ligand binding free energy calculation with AMOEBA Y Shi, D Jiao, MJ Schnieders, P Ren 2009 Annual International Conference of the IEEE Engineering in Medicine and …, 2009 | 20 | 2009 |
| Stereoselective synthesis of tetrahydrofuran lignans D Soorukram, M Pohmakotr, C Kuhakarn, V Reutrakul Synthesis 50 (24), 4746-4764, 2018 | 19 | 2018 |
| Molecular dynamics studies of modular polyketide synthase ketoreductase stereospecificity ML Mugnai, Y Shi, AT Keatinge-Clay, R Elber Biochemistry 54 (14), 2346-2359, 2015 | 17 | 2015 |
| Predicting water uptake in poly (perfluorosulfonic acids) using force field simulation methods X Li, F Li, Y Shi, Q Chen, H Sun Physical Chemistry Chemical Physics 12 (43), 14543-14552, 2010 | 14 | 2010 |
| Temperature dependence of the complexation mechanism of celecoxib and hydroxyl-β-cyclodextrin in aqueous solution PC Chiang, Y Shi, Y Cui Pharmaceutics 6 (3), 467-480, 2014 | 13 | 2014 |
| 6 Polarizable Force Fields for Scoring Protein-Ligand Interactions Jiajing Zhang, Yue Shi, and Pengyu Ren J Zhang, Y Shi, P Ren Protein-Ligand Interactions 53, 101, 2012 | 11 | 2012 |
| Exploring the relationship between sequences, structures, dynamical behaviors and functions of new type protein drugs: DARPins X Wu, Y Shi, P Ren, D Wang, G Li Current pharmaceutical design 19 (12), 2308-2317, 2013 | 1 | 2013 |
| Modeling the interaction and energetics of biological molecules with a polarizable force field Y Shi | | 2013 |
| Probing the Effect of Conformational Constraints on Binding AD Bowen, Y Shi 2012 SC Companion: High Performance Computing, Networking, Storage and …, 2012 | | 2012 |
| Thermodynamic effects of conformational constraints in protein-ligand interactions Y Shi, C Zhu, S Martin, P Ren ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 244, 2012 | | 2012 |
