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 |
|
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