Rice University

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Publications

Found 879 results
2011
Wang Y., Hess T.N, Jones V., Zhou J.Z, McNeil M.R, McCammon J.A.  2011.  Novel inhibitors of Mycobacterium tuberculosis dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) identified by virtual screening. Bioorgan. Medicinal Chem. Lett.. 21:7064-7067.
Yan D.L, Lenz P., Hwa T..  2011.  Overcoming Fluctuation and Leakage Problems in the Quantification of Intracellular 2-Oxoglutarate Levels in Escherichia coli. Appld. Enviro. Microbio.. 77:6763-6771.
Volman V., Bazhenov M., Sejnowski T.J.  2011.  Pattern of trauma determines the threshold for epileptic activity in a model of cortical deafferentation. Proc. Nat. Acad. Sci. USAProceedings of the National Academy of Sciences of the United States of America. 108:15402-15407.
Radford R.J, Lawrenz M., Nguyen P.C, McCammon J.A, Tezcan F.A.  2011.  Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites. Chem. Comm.. 47:313-315.
Durrant JD, de Oliveira CÈAugusto F, J. McCammon A.  2011.  POVME: An algorithm for measuring binding-pocket volumes. J. Mol. Graph. Model.. 29:773-776.
Craig P.O., Latzer J., Weinkam P., Hoffman R.M., Ferreiro D.U, Komives E.A, Wolynes P.G.  2011.  Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes. J. Am. Chem. Soc.. 133:17463-72.
Nichols S.E, Baron R., Ivetac A., McCammon J.A.  2011.  Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening. J. Chem. Info. Model.J. Chem. Info. Model.. 51:1439-1446.
Durrant J.D, de Oliveira C.AF, McCammon J.A.  2011.  Pyrone-Based Inhibitors of Metalloproteinase Types 2 and 3 May Work as ConformationSelective Inhibitors. Chem. Biol. Drug DesignChemical Biology & Drug Design. 78:191-198.
Hu B., Chen W., Levine H., Rappel W.J.  2011.  Quantifying Information Transmission in Eukaryotic Gradient Sensing and Chemotactic Response. Journal of Statistical PhysicsJournal of Statistical Physics. 142:1167-1186.
Hao Y., Zhang Z.J, Erickson D.W, Huang M., Huang Y.W, Li J.B, Hwa T., Shi H.L.  2011.  Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc. Nat. Acad. Sci. USAProceedings of the National Academy of Sciences of the United States of America. 108:12473-12478.
Ferreiro D.U, Hegler J.A, Komives E.A, Wolynes P.G.  2011.  On the role of frustration in the energy landscapes of allosteric proteins. Proc. Nat. Acad. Sci. USAProceedings of the National Academy of Sciences of the United States of America. 108:3499-3503.
Fitzgerald J.D, Rowekamp R.J., Sincich L.C., Sharpee T.O.  2011.  Second order dimensionality reduction using minimum and maximum mutual information models. Plos Comp. Biol.. 7:e1002249.
Hecht I., Levine H., Rappel W.J, Ben-Jacob E..  2011.  "Self-Assisted" Amoeboid Navigation in Complex Environments. Plos OnePlos One. 6:9.
Suzuki Y., Noel J.K, Onuchic J.N.  2011.  A semi-analytical description of protein folding that incorporates detailed geometrical information. Journal of Chemical PhysicsJournal of Chemical Physics. 134:13.
Liu C.L, Fu X.F, Liu L.L, Ren X.J, Chau C.KL, Li S.H, Xiang L., Zeng H.L, Chen G.H, Tang L.H et al..  2011.  Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science. 334:238-241.
Shklarsh A., Ariel G., Schneidman E., Ben-Jacob E..  2011.  Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions. Plos Comp. Biol.. 7
Hermsen R., Erickson D.W, Hwa T..  2011.  Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits. Plos Comp. Biol.. 7
Wang S.S, Wolynes P.G.  2011.  On the spontaneous collective motion of active matter. Proc. Nat. Acad. Sci. USAProceedings of the National Academy of Sciences of the United States of America. 108:15184-15189.
Hyeon C., Onuchic J.N.  2011.  A Structural Perspective on the Dynamics of Kinesin Motors. Biophys. J.. 101:2749-2759.
Volman V., Gerkin R.C..  2011.  Synaptic Scaling Stabilizes Persistent Activity Driven by Asynchronous Neurotransmitter Release. Neural Computation.
De Pitta M., Volman V., Berry H., Ben-Jacob E..  2011.  A Tale of Two Stories: Astrocyte Regulation of Synaptic Depression and Facilitation. Plos Comp. Biol.. 7
Volman V., Sejnowski T.J, Bazhenov M..  2011.  Topological basis of epileptogenesis in a model of severe cortical trauma. J. Neurophysiol.. 106:1933-1942.
Sharpee T.O., Nagel K.I., Doupe A.J..  2011.  Two-dimensional adaptation in the auditory forebrain. J Neurophys.. 106:1841-1861.
Stevenson J.D, Wolynes P.G.  2011.  The Ultimate Fate of Supercooled Liquids. Journal of Physical Chemistry AJournal of Physical Chemistry A. 115:3713-3719.
Romanowska J., McCammon J.A, Trylska J..  2011.  Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site. Plos Comp. Biol.Plos Computational Biology. 7:16.

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