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Yue Shi
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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
6872013
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
912012
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
882013
Multipole electrostatics in hydration free energy calculations
Y Shi, C Wu, JW Ponder, P Ren
Journal of computational chemistry 32 (5), 967-977, 2011
822011
Polarizable force fields for biomolecular modeling
Y Shi, P Ren, M Schnieders, JP Piquemal
Reviews in Computational Chemistry Volume 28, 51-86, 2015
582015
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
552012
Molecular docking simulations for macromolecularly imprinted polymers
DR Kryscio, Y Shi, P Ren, NA Peppas
Industrial & engineering chemistry research 50 (24), 13877-13884, 2011
352011
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
302012
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
242014
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
242012
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
202009
Stereoselective synthesis of tetrahydrofuran lignans
D Soorukram, M Pohmakotr, C Kuhakarn, V Reutrakul
Synthesis 50 (24), 4746-4764, 2018
182018
Molecular dynamics studies of modular polyketide synthase ketoreductase stereospecificity
ML Mugnai, Y Shi, AT Keatinge-Clay, R Elber
Biochemistry 54 (14), 2346-2359, 2015
162015
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
132010
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
112014
Polarizable force fields for scoring protein–ligand interactions
J Zhang, Y Shi, P Ren
Protein‐Ligand Interactions, 99-120, 2012
112012
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
12013
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
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Articles 1–20