Tongye Shen - Publications

Affiliations: 
2002 University of California, San Diego, La Jolla, CA 

51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Johnson QR, Lindsay RJ, Nellas RB, Shen T. Pressure induced conformational switch of an interfacial protein lipase. Proteins. PMID 26967808 DOI: 10.1002/Prot.25031  0.32
2015 Gu C, Shen T, An H, Yuan C, Zhou J, Ye Q, Liu T, Wang X, Zhang T. Combined therapy of Di-Huang-Yi-Zhi with Donepezil in patients with Parkinson's disease dementia. Neuroscience Letters. PMID 26297124 DOI: 10.1016/j.neulet.2015.08.019  0.32
2015 Johnson QR, Lindsay RJ, Petridis L, Shen T. Investigation of Carbohydrate Recognition via Computer Simulation. Molecules (Basel, Switzerland). 20: 7700-18. PMID 25927900 DOI: 10.3390/Molecules20057700  0.32
2015 Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. Mapping allostery through computational glycine scanning and correlation analysis of residue-residue contacts. Biochemistry. 54: 1534-41. PMID 25658131 DOI: 10.1021/Bi501152D  0.32
2015 Yang S, Shen T, Qi W. A gear fault diagnosis method based on gaborlet transform a tlas Journal of Computational Information Systems. 11: 1463-1470. DOI: 10.12733/jcis13533  0.64
2015 Yang S, Shen T, Qi W. A gear fault diagnosis method based on gaborlet transform a tlas Journal of Computational Information Systems. 11: 1463-1470. DOI: 10.12733/jcis13533  0.64
2015 Liu T, Shen T, Yang S, Jiang Z. Subwavelength focusing by binary multi-annular plates: Design theory and experiment Journal of Optics (United Kingdom). 17. DOI: 10.1088/2040-8978/17/3/035610  0.64
2015 Liu T, Shen T, Yang S, Jiang Z. Subwavelength focusing by binary multi-annular plates: Design theory and experiment Journal of Optics (United Kingdom). 17. DOI: 10.1088/2040-8978/17/3/035610  0.64
2014 Johnson QR, Lindsay RJ, Raval SR, Dobbs JS, Nellas RB, Shen T. Effects of branched O-glycosylation on a semiflexible peptide linker. The Journal of Physical Chemistry. B. 118: 2050-7. PMID 24533620 DOI: 10.1021/Jp410788R  0.32
2013 Nellas RB, Johnson QR, Shen T. Solvent-induced α- to 3(10)-helix transition of an amphiphilic peptide. Biochemistry. 52: 7137-44. PMID 24066804 DOI: 10.1021/Bi400537Z  0.32
2013 Shen T, Qi X, Nellas RB. Nucleation dynamics of active particles. The Journal of Physical Chemistry. B. 117: 12844-9. PMID 23819710 DOI: 10.1021/Jp402024S  0.32
2013 Qi X, Nellas RB, Byrn MW, Russell MH, Bible AN, Alexandre G, Shen T. Swimming motility plays a key role in the stochastic dynamics of cell clumping. Physical Biology. 10: 026005. PMID 23416991 DOI: 10.1088/1478-3975/10/2/026005  0.32
2012 Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, Gnanakaran S. A coarse-grained model for synergistic action of multiple enzymes on cellulose. Biotechnology For Biofuels. 5: 55. PMID 22853643 DOI: 10.1186/1754-6834-5-55  0.32
2012 Johnson QR, Nellas RB, Shen T. Solvent-dependent gating motions of an extremophilic lipase from Pseudomonas aeruginosa. Biochemistry. 51: 6238-45. PMID 22830585 DOI: 10.1021/Bi300557Y  0.32
2012 Nellas RB, Glover MM, Hamelberg D, Shen T. High-pressure effect on the dynamics of solvated peptides. The Journal of Chemical Physics. 136: 145103. PMID 22502549 DOI: 10.1063/1.3700183  0.32
2011 Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, et al. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. Plos Pathogens. 7: e1002209. PMID 21980282 DOI: 10.1371/Journal.Ppat.1002209  0.32
2011 Klein HC, Cheng X, Smith JC, Shen T. Transfer matrix approach to the hydrogen-bonding in cellulose Iα fibrils describes the recalcitrance to thermal deconstruction. The Journal of Chemical Physics. 135: 085106. PMID 21895224 DOI: 10.1063/1.3626274  0.32
2011 Yao J, Nellas RB, Glover MM, Shen T. Stability and sugar recognition ability of ricin-like carbohydrate binding domains. Biochemistry. 50: 4097-104. PMID 21510689 DOI: 10.1021/Bi102021P  0.32
2011 Wang S, Shen T, Wolynes PG. The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics. The Journal of Chemical Physics. 134: 014510. PMID 21219010 DOI: 10.1063/1.3518450  0.32
2010 Johnson Q, Doshi U, Shen T, Hamelberg D. Water's Contribution to the Energetic Roughness from Peptide Dynamics. Journal of Chemical Theory and Computation. 6: 2591-7. PMID 26616063 DOI: 10.1021/Ct100183S  0.32
2010 Bellesia G, Asztalos A, Shen T, Langan P, Redondo A, Gnanakaran S. In silico studies of crystalline cellulose and its degradation by enzymes. Acta Crystallographica. Section D, Biological Crystallography. 66: 1184-8. PMID 21041934 DOI: 10.1107/S0907444910029483  0.32
2010 Lynch RM, Rong R, Li B, Shen T, Honnen W, Mulenga J, Allen S, Pinter A, Gnanakaran S, Derdeyn CA. Subtype-specific conservation of isoleucine 309 in the envelope V3 domain is linked to immune evasion in subtype C HIV-1 infection. Virology. 404: 59-70. PMID 20494390 DOI: 10.1016/J.Virol.2010.04.010  0.32
2009 Shen T, Gnanakaran S. The stability of cellulose: a statistical perspective from a coarse-grained model of hydrogen-bond networks. Biophysical Journal. 96: 3032-40. PMID 19383449 DOI: 10.1016/J.Bpj.2008.12.3953  0.32
2009 Lynch RM, Shen T, Gnanakaran S, Derdeyn CA. Appreciating HIV type 1 diversity: subtype differences in Env. Aids Research and Human Retroviruses. 25: 237-48. PMID 19327047 DOI: 10.1089/Aid.2008.0219  0.32
2008 Shen T, Hamelberg D. A statistical analysis of the precision of reweighting-based simulations. The Journal of Chemical Physics. 129: 034103. PMID 18647012 DOI: 10.1063/1.2944250  0.32
2008 Shen T, Zong C, Portman JJ, Wolynes PG. Variationally determined free energy profiles for structural models of proteins: characteristic temperatures for folding and trapping. The Journal of Physical Chemistry. B. 112: 6074-82. PMID 18376882 DOI: 10.1021/Jp076280N  0.32
2008 Lätzer J, Shen T, Wolynes PG. Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles. Biochemistry. 47: 2110-22. PMID 18198897 DOI: 10.1021/Bi701350V  0.32
2007 Lu T, Shen T, Bennett MR, Wolynes PG, Hasty J. Phenotypic variability of growing cellular populations. Proceedings of the National Academy of Sciences of the United States of America. 104: 18982-7. PMID 18025471 DOI: 10.1073/Pnas.0706115104  0.32
2007 Hamelberg D, Shen T, McCammon JA. A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw. Proceedings of the National Academy of Sciences of the United States of America. 104: 14947-51. PMID 17823247 DOI: 10.1073/Pnas.0703151104  0.32
2007 Zong C, Wilson CJ, Shen T, Wittung-Stafshede P, Mayo SL, Wolynes PG. Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin. Proceedings of the National Academy of Sciences of the United States of America. 104: 3159-64. PMID 17301232 DOI: 10.1073/Pnas.0611149104  0.32
2006 Lu T, Shen T, Zong C, Hasty J, Wolynes PG. Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space. Proceedings of the National Academy of Sciences of the United States of America. 103: 16752-7. PMID 17071742 DOI: 10.1073/Pnas.0607698103  0.32
2006 Hamelberg D, Shen T, McCammon JA. Insight into the role of hydration on protein dynamics. The Journal of Chemical Physics. 125: 094905. PMID 16965117 DOI: 10.1063/1.2232131  0.32
2006 Shen T, Hamelberg D, McCammon JA. Elasticity of peptide omega bonds. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 73: 041908. PMID 16711837 DOI: 10.1103/Physreve.73.041908  0.32
2006 Zong C, Wilson CJ, Shen T, Wolynes PG, Wittung-Stafshede P. Phi-value analysis of apo-azurin folding: comparison between experiment and theory. Biochemistry. 45: 6458-66. PMID 16700556 DOI: 10.1021/Bi060025W  0.32
2006 Zong C, Lu T, Shen T, Wolynes PG. Nonequilibrium self-assembly of linear fibers: microscopic treatment of growth, decay, catastrophe and rescue. Physical Biology. 3: 83-92. PMID 16582473 DOI: 10.1088/1478-3975/3/1/009  0.32
2006 Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA. Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophysical Journal. 90: 3880-5. PMID 16533835 DOI: 10.1529/Biophysj.105.074575  0.32
2006 Shen T, Wolynes PG. Statistical mechanics of a cat's cradle New Journal of Physics. 8. DOI: 10.1088/1367-2630/8/11/273  0.32
2005 Shen T, Wolynes PG. Nonequilibrium statistical mechanical models for cytoskeletal assembly: towards understanding tensegrity in cells. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 041927. PMID 16383440 DOI: 10.1103/Physreve.72.041927  0.32
2005 Shen T, Zong C, Hamelberg D, McCammon JA, Wolynes PG. The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 19: 1389-95. PMID 16126906 DOI: 10.1096/Fj.04-3590Hyp  0.32
2005 Hamelberg D, Shen T, Andrew McCammon J. Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations. The Journal of Chemical Physics. 122: 241103. PMID 16035738 DOI: 10.1063/1.1942487  0.32
2005 Shen T, Hofmann CP, Oliveberg M, Wolynes PG. Scanning malleable transition state ensembles: comparing theory and experiment for folding protein U1A. Biochemistry. 44: 6433-9. PMID 15850377 DOI: 10.1021/Bi0500170  0.32
2005 Levy Y, Cho SS, Shen T, Onuchic JN, Wolynes PG. Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery. Proceedings of the National Academy of Sciences of the United States of America. 102: 2373-8. PMID 15701699 DOI: 10.1073/Pnas.0409572102  0.32
2005 Hamelberg D, Shen T, McCammon JA. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. Journal of the American Chemical Society. 127: 1969-74. PMID 15701032 DOI: 10.1021/Ja0446707  0.32
2004 Shen T, Wolynes PG. Stability and dynamics of crystals and glasses of motorized particles. Proceedings of the National Academy of Sciences of the United States of America. 101: 8547-50. PMID 15173584 DOI: 10.1073/Pnas.0402602101  0.32
2003 Shen T, Wong CF, McCammon JA. Brownian dynamics simulation of helix-capping motifs. Biopolymers. 70: 252-9. PMID 14517913 DOI: 10.1002/Bip.10466  0.32
2002 Shen T, Canino LS, McCammon JA. Unfolding proteins under external forces: a solvable model under the self-consistent pair contact probability approximation. Physical Review Letters. 89: 068103. PMID 12190614 DOI: 10.1103/Physrevlett.89.068103  0.32
2002 Canino LS, Shen T, McCammon JA. Changes in flexibility upon binding: Application of the self-consistent pair contact probability method to protein-protein interactions Journal of Chemical Physics. 117: 9927-9933. DOI: 10.1063/1.1517605  0.32
2001 Shen T, Wong CF, McCammon JA. Atomistic Brownian dynamics simulation of peptide phosphorylation Journal of the American Chemical Society. 123: 9107-9111. PMID 11552818 DOI: 10.1021/ja010190t  0.32
2001 Tai K, Shen T, Börjesson U, Philippopoulos M, McCammon JA. Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophysical Journal. 81: 715-24. PMID 11463620 DOI: 10.1016/S0006-3495(01)75736-0  0.32
2001 Shen TY, Tai K, McCammon JA. Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 041902. PMID 11308872 DOI: 10.1103/Physreve.63.041902  0.32
2000 Wlodek ST, Shen T, McCammon JA. Electrostatic steering of substrate to acetylcholinesterase: Analysis of field fluctuations Biopolymers. 53: 265-271. PMID 10679631 DOI: 10.1002/(Sici)1097-0282(200003)53:3<265::Aid-Bip6>3.0.Co;2-N  0.32
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