Search Results - "Bruccoleri, Robert E"

Genome assembly of the bearded iris, Iris pallida Lam by Bruccoleri, Robert E, Oakeley, Edward J, Faust, Ann Marie E, Altorfer, Marc, Dessus-Babus, Sophie, Burckhardt, David, Oertli, Mevion, Naumann, Ulrike, Petersen, Frank, Wong, Joanne

“…Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest…”
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Transcriptional profiling of the dose response: a more powerful approach for characterizing drug activities by Ji, Rui-Ru, de Silva, Heshani, Jin, Yisheng, Bruccoleri, Robert E, Cao, Jian, He, Aiqing, Huang, Wenjun, Kayne, Paul S, Neuhaus, Isaac M, Ott, Karl-Heinz, Penhallow, Becky, Cockett, Mark I, Neubauer, Michael G, Siemers, Nathan O, Ross-Macdonald, Petra

“…The dose response curve is the gold standard for measuring the effect of a drug treatment, but is rarely used in genomic scale transcriptional profiling due to…”
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Conserved Fungal Genes as Potential Targets for Broad-Spectrum Antifungal Drug Discovery by Liu, Mengping, Healy, Matthew D, Dougherty, Brian A, Esposito, Kim M, Maurice, Trina C, Mazzucco, Charles E, Bruccoleri, Robert E, Davison, Daniel B, Frosco, Marybeth, Barrett, John F, Wang, Ying-Kai

“…Classifications Services EC Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit…”
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SDRS—an algorithm for analyzing large-scale dose–response data by Ji, Rui-Ru, Siemers, Nathan O, Lei, Ming, Schweizer, Liang, Bruccoleri, Robert E

“…Dose–response information is critical to understanding drug effects, yet analytical methods for dose–response assays cannot cope with the dimensionality of…”
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Structure of antibody hypervariable loops reproduced by a conformational search algorithm by Bruccoleri, Robert E, Haber, Edgar, Novotný, Ji í

“…The antigen-combining site of antibody molecules consists of six separate loops supported by a conserved beta-sheet framework; antibody specificity arises from…”
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Structural and Dynamic Properties of a .beta.-Hairpin-Forming Linear Peptide. 1. Modeling Using Ensemble-Averaged Constraints by Constantine, Keith L, Mueller, Luciano, Andersen, Niels H, Tong, Hui, Wandler, Charles F, Friedrichs, Mark S, Bruccoleri, Robert E

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FDR-FET: an optimizing gene set enrichment analysis method by Ji, Rui-Ru, Ott, Karl-Heinz, Yordanova, Roumyana, Bruccoleri, Robert E

“…Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated…”
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On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5 by Novotny, Jiri, Bruccoleri, Robert E, Saul, Frederick A

“…Using X-ray coordinates of antigen-antibody complexes McPC 603, D1.3, and HyHEL-5, we made semiquantitative estimates of Gibbs free energy changes (delta G)…”
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Prediction of the folding of short polypeptide segments by uniform conformational sampling by Bruccoleri, R E, Karplus, M

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Chain closure with bond angle variations by Bruccoleri, Robert E, Karplus, Martin

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Correlation among sites of limited proteolysis, enzyme accessibility and segmental mobility by Novotný, Jiří, Bruccoleri, Robert E.

“…The relationship among accessibility to an enzyme, flexibility, and limited proteolysis was explored. Regions accessible to large probes, comparable in size…”
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Structural and Dynamic Properties of a .beta.-Hairpin-Forming Linear Peptide. 2. 13C NMR Relaxation Analysis by Friedrichs, Mark S, Stouch, Terry R, Bruccoleri, Robert E, Mueller, Luciano, Constantine, Keith L

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Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2 by Bassolino‐Klimas, Donna, Bruccoleri, Robert E., Subramaniam, Shankar

“…A model structure has been constructed for a monoclonal anti‐dinitrophenyl antibody. The antibody, ANO2, has been sequenced and cloned (Anglister, J., Frey,…”
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Antigenicity of Myohemerythrin by Novotny, Jiri, Bruccoleri, Robert E., Carlson, William D., Handschumacher, Mark, Haber, Edgar

“…A study of antigenicity of the protein myohemerythrin showed that the most frequently recognized sites form three-dimensional superassemblies characterized by…”
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Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities: e1000512 by Ji, Rui-Ru, Silva, Heshani de, Jin, Yisheng, Bruccoleri, Robert E, Cao, Jian, He, Aiqing, Huang, Wenjun, Kayne, Paul S, Neuhaus, Isaac M, Ott, Karl-Heinz, Penhallow, Becky, Cockett, Mark I, Neubauer, Michael G, Siemers, Nathan O, Ross-Macdonald, Petra

“…The dose response curve is the gold standard for measuring the effect of a drug treatment, but is rarely used in genomic scale transcriptional profiling due to…”
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Concordance analysis of microbial genomes by Bruccoleri, Robert E., Dougherty, Thomas J., Davison, Daniel B.

“…The set of proteins which are conserved across families of microbes contain important targets of new anti-microbial agents. We have developed a simple and…”
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Empirical free energy calculations: a blind test and further improvements to the method by Novotny, J, Bruccoleri, R E, Davis, M, Sharp, K A

“…Empirical Gibbs functions estimate free energies of non-covalent reactions (deltaG) from atomic coordinates of reaction products (e.g. antibody-antigen…”
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Finite difference Poisson-Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing by Bruccoleri, Robert E., Novotny, Jiri, Davis, Malcolm E., Sharp, Kim A.

“…A common problem in the calculation of electrostatic potentials with the Poisson‐Boltzmann equation using finite difference methods is the effect of molecular…”
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Protein Engineering of Antibody Binding Sites: Recovery of Specific Activity in an Anti-Digoxin Single-Chain Fv Analogue Produced in Escherichia coli by Huston, James S., Levinson, Douglas, Mudgett-Hunter, Meredith, Tai, Mei-Sheng, Novotný, Jiří, Margolies, Michael N., Ridge, Richard J., Bruccoleri, Robert E., Haber, Edgar, Crea, Roberto, Oppermann, Hermann

“…A biosynthetic antibody binding site, which incorporated the variable domains of anti-digoxin monoclonal antibody 26-10 in a single polypeptide chain (Mr =…”
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Conformational sampling using high-temperature molecular dynamics by Bruccoleri, R E, Karplus, M

“…High-temperature molecular dynamics as a method for conformational search was explored on the antigen combining site of McPC 603, a phosphorylcholine binding…”
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