Yue Shi
TitreCitée parAnnée
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
3882013
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
742012
Multipole electrostatics in hydration free energy calculations
Y Shi, C Wu, JW Ponder, P Ren
Journal of computational chemistry 32 (5), 967-977, 2011
672011
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
542013
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
452012
Polarizable force fields for biomolecular modeling
Y Shi, P Ren, M Schnieders, JP Piquemal
Reviews in computational chemistry 28 (51), 2015
322015
Engineering in Medicine and Biology Society, 2009. EMBC 2009
Y Shi, D Jiao, MJ Schnieders, P Ren
Annual International Conference of the IEEE, 2328-2331, 2009
282009
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
222012
Molecular docking simulations for macromolecularly imprinted polymers
DR Kryscio, Y Shi, P Ren, NA Peppas
Industrial & engineering chemistry research 50 (24), 13877-13884, 2011
192011
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
182012
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
162009
Polarizable force fields for scoring protein–ligand interactions
J Zhang, Y Shi, P Ren
Protein‐Ligand Interactions, 99-120, 2012
142012
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
112014
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
112010
Molecular dynamics studies of modular polyketide synthase ketoreductase stereospecificity
ML Mugnai, Y Shi, AT Keatinge-Clay, R Elber
Biochemistry 54 (14), 2346-2359, 2015
92015
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
92014
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
On the Microscopic Reasons for Stereospecificity of the Enzyme Ketoreductase: A Molecular Dynamics Study: 451
R Elber, A Keatinge-Clay, M Mugnai, Y Shi
Protein Science 22, 2013
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
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