Rice University

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Publications

Found 879 results
2011
Suzuki Y., Dudko O.K.  2011.  Biomolecules under mechanical stress: A simple mechanism of complex behavior. Journal of Chemical Physics. 134
Dlugosz M., Huber G.A, McCammon J.A, Trylska J..  2011.  Brownian Dynamics Study of the Association Between the 70S Ribosome and Elongation Factor G. BiopolymersBiopolymers. 95:616-627.
Sikora M., Sulkowska J.I, Witkowski B.S, Cieplak M..  2011.  BSDB: the biomolecule stretching database. Nucl. Acids Res.. 39:D443-D450.
Wang S.S, Wolynes P.G.  2011.  Communication: Effective temperature and glassy dynamics of active matter. Journal of Chemical PhysicsJournal of Chemical Physics. 135:4.
Skjaerven L., Grant B., Muga A., Teigen K., McCammon J.A, Reuter N., Martinez A..  2011.  Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations. Plos Comp. Biol.Plos Computational Biology. 7:14.
Feng J., Walter N.G, Brooks C.L.  2011.  Cooperative and Directional Folding of the preQ(1) Riboswitch Aptamer Domain. J. Am. Chem. Soc.J. Am. Chem. Soc.. 133:4196-4199.
Durrant J.D, Friedman A.J, McCammon J.A.  2011.  CrystalDock: A Novel Approach to Fragment-Based Drug Design. J. Chem. Info. Model.. 51:2573-2580.
Quinn J.C, Abarbanel H.DI.  2011.  Data assimilation using a GPU accelerated path integral Monte Carlo approach. J Comp. Phys.. 230:8168-8178.
Hu B., Levine H., Rappel W.J.  2011.  Design principles and specificity in biological networks with cross activation. Physical Biology. 8:026001.
Li B., Cheng X.L, Zhang Z.F.  2011.  DIELECTRIC BOUNDARY FORCE IN MOLECULAR SOLVATION WITH THE POISSON-BOLTZMANN FREE ENERGY: A SHAPE DERIVATIVE APPROACH. SIAM J. Applied Math.. 71:2093-2111.
Mereghetti P., Kokh D., McCammon J.A, Wade R.C.  2011.  Diffusion and association processes in biological systems: theory, computation and experiment. Bmc Biophysics. 4
Morcos F., Pagnani A., Lunt B., Bertolino A., Marks D.S, Sander C., Zecchina R., Onuchic J.N, Hwa T., Weigt M..  2011.  Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc. Nat. Acad. Sci. USA. 108:E1293-E1301.
Procaccini A., Lunt B., Szurmant H., Hwa T., Weigt M..  2011.  Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks. Plos One. 6
Volman V., Behrens M.M, Sejnowski T.J.  2011.  Downregulation of Parvalbumin at Cortical GABA Synapses Reduces Network Gamma Oscillatory Activity. Journal of Neuroscience. 31:18137-18148.
Abarbanel H.D., Bryant P., Gill P.E., Kostuk M., Rofeh J., Singer Z., Toth B., Wong E..  2011.  The Dynamic Brain: An Exploration of Neuronal Variability and Its Functional Significance.
Toth B.A, Kostuk M., Meliza C.D, Margoliash D., Abarbanel H.DI.  2011.  Dynamical estimation of neuron and network properties I: variational methods. Biological Cybernetics. 105:217-237.
Lawrenz M., Baron R., Wang Y., McCammon J.A.  2011.  Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies. J. Chem. Theor. Comp.J. Chem. Theor. Comp.. 7:2224-2232.
Hu B., Kessler D.A, Rappel W.J, Levine H..  2011.  Effects of Input Noise on a Simple Biochemical Switch. Physical Review Letters. 107
Grant B.J, Gheorghe D.M, Zheng W.J, Alonso M., Huber G., Dlugosz M., McCammon J.A, Cross R.A.  2011.  Electrostatically Biased Binding of Kinesin to Microtubules. Plos Biology. 9
Jeanne J.M, Thompson J.V, Sharpee T.O, Gentner T.Q.  2011.  Emergence of Learned Categorical Representations within an Auditory Forebrain Circuit. Journal of NeuroscienceJournal of Neuroscience. 31:2595-2606.
Wang Y., Markwick P.RL, de Oliveira C.AF, McCammon J.A.  2011.  Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. J. Chem. Theor. Comp.. 7:3199-3207.
Whitford P.C, Ahmed A., Yu Y.A, Hennelly S.P, Tama F., Spahn C.MT, Onuchic J.N, Sanbonmatsu K.Y.  2011.  Excited states of ribosome translocation revealed through integrative molecular modeling. Proc. Nat. Acad. Sci. USA. 108:18943-18948.
Williams S.L, de Oliveira C.AF, Vazquez H., McCammon J.A.  2011.  From Zn to Mn: The Study of Novel Manganese-binding Groups in the Search for New Drugs against Tuberculosis. Chem. Biol. Drug DesignChemical Biology & Drug Design. 77:117-123.
Li W.F, Wolynes P.G, Takada S..  2011.  Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins. Proc. Nat. Acad. Sci. USA. 108:3504-3509.
Volman V., Perc M., Bazhenov M..  2011.  Gap Junctions and Epileptic Seizures - Two Sides of the Same Coin? Plos One. 6

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