Search Results - "Honig, B."

Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation:  Multiple Dielectric Constants and Multivalent Ions by Rocchia, W, Alexov, E, Honig, B

“…A new version of the DelPhi program, which provides numerical solutions to the nonlinear Poisson−Boltzmann (PB) equation, is reported. The program can divide…”
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Maladaptive positive feedback production of ChREBPβ underlies glucotoxic β-cell failure by Katz, Liora S., Brill, Gabriel, Zhang, Pili, Kumar, Anil, Baumel-Alterzon, Sharon, Honig, Lee B., Gómez-Banoy, Nicolás, Karakose, Esra, Tanase, Marius, Doridot, Ludivine, Alvarsson, Alexandra, Davenport, Bennett, Wang, Peng, Lambertini, Luca, Stanley, Sarah A., Homann, Dirk, Stewart, Andrew F., Lo, James C., Herman, Mark A., Garcia-Ocaña, Adolfo, Scott, Donald K.

“…Preservation and expansion of β-cell mass is a therapeutic goal for diabetes. Here we show that the hyperactive isoform of carbohydrate response-element…”
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PredUs: a web server for predicting protein interfaces using structural neighbors by Zhang, Qiangfeng Cliff, Deng, Lei, Fisher, Markus, Guan, Jihong, Honig, Barry, Petrey, Donald

“…We describe PredUs, an interactive web server for the prediction of protein-protein interfaces. Potential interfacial residues for a query protein are…”
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Author Correction: Maladaptive positive feedback production of ChREBPβ underlies glucotoxic β-cell failure by Katz, Liora S., Brill, Gabriel, Zhang, Pili, Kumar, Anil, Baumel-Alterzon, Sharon, Honig, Lee B., Gómez-Banoy, Nicolás, Karakose, Esra, Tanase, Marius, Doridot, Ludivine, Alvarsson, Alexandra, Davenport, Bennett, Wang, Peng, Lambertini, Luca, Stanley, Sarah A., Homann, Dirk, Stewart, Andrew F., Lo, James C., Herman, Mark A., Garcia-Ocaña, Adolfo, Scott, Donald K.

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Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure by Joshi, Rohit, Passner, Jonathan M., Rohs, Remo, Jain, Rinku, Sosinsky, Alona, Crickmore, Michael A., Jacob, Vinitha, Aggarwal, Aneel K., Honig, Barry, Mann, Richard S.

“…The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of…”
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Type II Cadherin Ectodomain Structures: Implications for Classical Cadherin Specificity by Patel, Saurabh D., Ciatto, Carlo, Chen, Chien Peter, Bahna, Fabiana, Rajebhosale, Manisha, Arkus, Natalie, Schieren, Ira, Jessell, Thomas M., Honig, Barry, Price, Stephen R., Shapiro, Lawrence

“…Type I and II classical cadherins help to determine the adhesive specificities of animal cells. Crystal-structure determination of ectodomain regions from…”
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Seabird bycatch in the pelagic longline fishery off southern Africa by Petersen, S L, Honig, M B, Ryan, P G, Underhill, L G

“…The waters around South Africa provide rich foraging opportunities for pelagic seabirds. They also support a pelagic longline fleet targeting tunas Thunnus…”
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Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results by Ben-Tal, N., Honig, B., Peitzsch, R.M., Denisov, G., McLaughlin, S.

“…We measured directly the binding of Lys3, Lys5, and Lys7 to vesicles containing acidic phospholipids. When the vesicles contain 33% acidic lipids and the…”
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Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis by Norel, Raquel, Sheinerman, Felix, Petrey, Donald, Honig, Barry

“…The methods of continuum electrostatics are used to calculate the binding free energies of a set of protein–protein complexes including experimentally…”
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Flt3L and TK gene therapy eradicate multifocal glioma in a syngeneic glioblastoma model by King, Gwendalyn D, Muhammad, A K M Ghulam, Curtin, James F, Barcia, Carlos, Puntel, Mariana, Liu, Chunyan, Honig, Sarah B, Candolfi, Marianela, Mondkar, Sonali, Lowenstein, Pedro R, Castro, Maria G

“…The disseminated characteristics of human glioblastoma multiforme (GBM) make it a particularly difficult tumor to treat with long-term efficacy. Most…”
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A free energy analysis of nucleic acid base stacking in aqueous solution by Friedman, R.A., Honig, B.

“…This paper reports a theoretical study of the free energy contributions to nucleic acid base stacking in aqueous solution. Electrostatic interactions are…”
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Declarations of Independence: Arendt and Derrida on the Problem of Founding a Republic by Honig, B.

“…Beginning with Hannah Arendt's depiction of the American Revolution and founding, I critically examine Arendt's reading of the Declaration of Independence,…”
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Free energy determinants of tertiary structure and the evaluation of protein models by PETREY, DONALD, HONIG, BARRY

“…We develop a protocol for estimating the free energy difference between different conformations of the same polypeptide chain. The conformational free energy…”
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Membrane Binding of Peptides Containing Both Basic and Aromatic Residues. Experimental Studies with Peptides Corresponding to the Scaffolding Region of Caveolin and the Effector Region of MARCKS by Arbuzova, Anna, Wang, Libo, Wang, Jiyao, Hangyás-Mihályné, Gyöngyi, Murray, Diana, Honig, Barry, McLaughlin, Stuart

“…We have studied the binding of peptides containing both basic and aromatic residues to phospholipid vesicles. The peptides caveolin(92−101) and MARCKS(151−175)…”
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On the calculation of binding free energies using continuum methods: Application to MHC class I protein‐peptide interactions by Froloff, Nicolas, Windemuth, Andreas, Honig, Barry

“…This paper describes a methodology to calculate the binding free energy (ΔG) of a protein‐ligand complex using a continuum model of the solvent. A formal…”
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Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis by Lancaster, C.R., Michel, H., Honig, B., Gunner, M.R.

“…Based on new Rhodopseudomonas (Rp.) viridis reaction center (RC) coordinates with a reliable structure of the secondary acceptor quinone (QB) site, a continuum…”
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HB-EGF Signaling Is Required for Glucose-Induced Pancreatic β-Cell Proliferation in Rats by Maachi, Hasna, Fergusson, Grace, Ethier, Melanie, Brill, Gabriel N, Katz, Liora S, Honig, Lee B, Metukuri, Mallikarjuna R, Scott, Donald K, Ghislain, Julien, Poitout, Vincent

“…The molecular mechanisms of β-cell compensation to metabolic stress are poorly understood. We previously observed that nutrient-induced β-cell proliferation in…”
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The Wilson disease gene is a copper transporting ATPase with homology to the Menkes disease gene by Tanzi, R.E, Petrukhin, K, Chernov, I, Pellequer, J.L, Wasco, W, Ross, B, Romano, D.M, Parano, E, Pavone, L, Brzustowicz, L.M, Devoto, M, Peppercorn, J, Bush, A.I, Sternlieb, I, Pirastu, M, Gusella, J.F, Evgrafov, O, Penchaszadeh, G.K, Honig, B, Edelman, I.S, Soares, M.B, Scheinberg, I.H, Gilliam, T.C

“…Wilson disease (WD) is an autosomal recessive disorder characterized by the toxic accumulation of copper in a number of organs, particularly the liver and…”
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Free-energy determinants of alpha-helix insertion into lipid bilayers by Ben-Tal, N., Ben-Shaul, A., Nicholls, A., Honig, B.

“…A detailed treatment is provided of the various free-energy terms that contribute to the transfer of a polyalanine alpha-helix from the aqueous phase into…”
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Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles by Ben-Tal, N., Honig, B., Miller, C., McLaughlin, S.

“…We previously applied the Poisson-Boltzmann equation to atomic models of phospholipid bilayers and basic peptides to calculate their electrostatic interactions…”
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