Rice University

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Publications

Found 879 results
2011
McCammon J.A.  2011.  Gated Diffusion-controlled Reactions. Bmc Biophysics. 4
McHale P., Mizutani C.M, Kosman D., MacKay D.L, Belu M., Hermann A., McGinnis W., Bier E., Hwa T..  2011.  Gene length may contribute to graded transcriptional responses in the Drosophila embryo. Devel. Biol.. 360:230-240.
Klumpp S..  2011.  Growth-Rate Dependence Reveals Design Principles of Plasmid Copy Number Control. Plos One. 6
Durrant J.D, McCammon J.A.  2011.  HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. J. Mol. Graph. Model.. 31:5-9.
Sharpee T.O, Atencio C.A, Schreiner C.E.  2011.  Hierarchical representations in the auditory cortex. Curr. Opin. Neurobiol.. 21:761-767.
Hu B., Chen W., Rappel W.J, Levine H..  2011.  How geometry and internal bias affect the accuracy of eukaryotic gradient sensing. Physical Review EPhysical Review E. 83:9.
McLaughlin W.A, Hou T.J, Taylor S.S, Wang W..  2011.  The identification of novel cyclic AMP-dependent protein kinase anchoring proteins using bioinformatic filters and peptide arrays. Protein Engineering Design & SelectionProtein Engineering Design & Selection. 24:333-339.
Bucher D., Grant B.J, McCammon J.A.  2011.  Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein Biochemistry. 50:10530-10539.
Baxter E.L, Jennings P.A, Onuchic J.N.  2011.  Interdomain communication revealed in the diabetes drug target mitoNEET. Proc. Nat. Acad. Sci. USA. 108:5266-5271.
Li B., Shopple J..  2011.  An Interface-Fitted Finite Element Level Set Method with Application to Solidification and Solvation. Comm. Comp. Phys.. 10:32-56.
Wang S.S, Shen T.Y, Wolynes P.G.  2011.  The interplay of nonlinearity and architecture in equilibrium cytoskeletal mechanics. Journal of Chemical PhysicsJournal of Chemical Physics. 134
de Oliveira C.AF, Grant B.J, Zhou M., McCammon J.A.  2011.  Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation. Plos Comp. Biol.. 7
Dudko O.K, Graham T.GW, Best R.B.  2011.  Locating the Barrier for Folding of Single Molecules under an External Force. Physical Review Letters. 107
Ferreira F.M, Oliveira L.C, Germino G.G, Onuchic J.N, Onuchic L.F.  2011.  Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain. Proc. Nat. Acad. Sci. USA. 108:9833-9838.
Zhou S.G, Wang Z.M, Li B..  2011.  Mean-field description of ionic size effects with nonuniform ionic sizes: A numerical approach. Physical Review EPhysical Review E. 84:13.
Williams S.L, Blachly P.G, McCammon J.A.  2011.  Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study. Proteins-Structure Function and Bioinformatics. 79:3381-3388.
Fitzgerald J.D, Sincich L.C, Sharpee T.O.  2011.  Minimal Models of Multidimensional Computations. Plos Comp. Biol.Plos Computational Biology. 7:8.
Durrant J.D, McCammon J.A.  2011.  Molecular dynamics simulations and drug discovery. Bmc Biology. 9
Baron R., Binda C., Tortorici M., McCammon J.A, Mattevi A..  2011.  Molecular Mimicry and Ligand Recognition in Binding and Catalysis by the Histone Demethylase LSD1-CoREST Complex. StructureStructure. 19:212-220.
Ivetac A., McCammon J.A.  2011.  Molecular Recognition in the Case of Flexible Targets. Curr. Pharmaceutical Design. 17:1663-1671.
Madi A., Kenett D.Y, Bransburg-Zabary S., Merbl Y., Quintana F.J, Tauber A.I, Cohen I.R, Ben-Jacob E..  2011.  Network Theory Analysis of Antibody-Antigen Reactivity Data: The Immune Trees at Birth and Adulthood. Plos OnePlos One. 6:11.
Durrant J.D, McCammon J.A.  2011.  NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. J. Chem. Info. Model.. 51:2897-2903.
Durrant J.D, McCammon J.A.  2011.  NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes. J. Chem. Info. Model.J. Chem. Info. Model.. 50:1865-1871.
Durrant J.D, Cao R., Gorfe A.A, Zhu W., Li J.K, Sankovsky A., Oldfield E., McCammon J.A.  2011.  Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design. Chem. Biol. Drug Design. 78:323-332.
Grant B.J, Lukman S., Hocker H.J, Sayyah J., Brown J.H, McCammon J.A, Gorfe A.A.  2011.  Novel Allosteric Sites on Ras for Lead Generation. Plos One. 6

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