☰

Tongye Shen - Publications

Affiliations: 
2002 University of California, San Diego, La Jolla, CA 
Tree Info Similar researchers PubMed Report error

35 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
2020 Das P, Golloshi R, McCord RP, Shen T. Using contact statistics to characterize structure transformation of biopolymer ensembles. Physical Review. E. 101: 012419. PMID 32069653 DOI: 10.1103/Physreve.101.012419  0.306
2018 Pham B, Lindsay RJ, Shen T. Effector Binding-Directed Dimerization and Dynamic Communication between Allosteric Sites of Ribonucleotide Reductase. Biochemistry. PMID 30571104 DOI: 10.1021/Acs.Biochem.8B01131  0.332
2018 Lindsay RJ, Pham B, Shen T, McCord RP. Characterizing the 3D structure and dynamics of chromosomes and proteins in a common contact matrix framework. Nucleic Acids Research. PMID 29992238 DOI: 10.1093/Nar/Gky604  0.301
2018 Johnson QR, Lindsay RJ, Shen T. CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue-residue associations. Journal of Computational Chemistry. PMID 29464733 DOI: 10.1002/Jcc.25192  0.343
2018 Lindsay RJ, Siess J, Lohry DP, McGee TS, Ritchie JS, Johnson QR, Shen T. Characterizing protein conformations by correlation analysis of coarse-grained contact matrices. The Journal of Chemical Physics. 148: 025101. PMID 29331124 DOI: 10.1063/1.5004141  0.333
2016 Lindsay RJ, Johnson QR, Evangelista W, Nellas RB, Shen T. DMSO enhanced conformational switch of an interfacial enzyme. Biopolymers. PMID 27463323 DOI: 10.1002/Bip.22924  0.317
2016 Clark AK, Wilder JH, Grayson AW, Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor. The Journal of Physical Chemistry. B. PMID 27110634 DOI: 10.1021/Acs.Jpcb.6B02057  0.305
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  0.321
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  0.308
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  0.354
2015 Shen T, Wong CF. Brownian dynamics simulation of peptides with the University of Houston Brownian Dynamics (UHBD) program. Methods in Molecular Biology (Clifton, N.J.). 1268: 75-87. PMID 25555722 DOI: 10.1007/978-1-4939-2285-7_5  0.316
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  0.351
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  0.303
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  0.306
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  0.309
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  0.354
2009 Shen T, Langan P, French AD, Johnson GP, Gnanakaran S. Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence. Journal of the American Chemical Society. 131: 14786-94. PMID 19824731 DOI: 10.1021/Ja9034158  0.337
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  0.305
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  0.328
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  0.344
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  0.319
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  0.332
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  0.332
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  0.305
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  0.322
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  0.301
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  0.335
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  0.328
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  0.497
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  0.339
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  0.36
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  0.31
2002 Tai K, Shen T, Henchman RH, Bourne Y, Marchot P, McCammon JA. Mechanism of acetylcholinesterase inhibition by fasciculin: a 5-ns molecular dynamics simulation. Journal of the American Chemical Society. 124: 6153-61. PMID 12022850 DOI: 10.1021/Ja017310H  0.348
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  0.332
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  0.324
Show low-probability matches.