Browsing Biomolecular Engineering Research Center by Title

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Browsing Biomolecular Engineering Research Center by Title

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  • Constraining Ribosomal RNA Conformational Space
    Favaretto, Paola; Bhutkar, Arjun; Smith, Temple F. (Oxford University Press, 2005-09-09)
    Despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal RNA (rRNA) is able to find the correct and universally conserved core fold. This study reports a computational ...
  • GTPases and the Origin of the Ribosome
    Hartman, Hyman; Smith, Temple F (BioMed Central, 2010-5-20)
    BACKGROUND. This paper is an attempt to trace the evolution of the ribosome through the evolution of the universal P-loop GTPases that are involved with the ribosome in translation and with the attachment of the ribosome ...
  • Inferring Genome-Scale Rearrangement Phylogeny and Ancestral Gene Order: A Drosophila Case Study
    Bhutkar, Arjun; Gelbart, William M; Smith, Temple F (BioMed Central, 2007-11-8)
    A simple, fast, and biologically inspired computational approach for inferring genome-scale rearrangement phylogeny and ancestral gene order has been developed. This has been applied to eight Drosophila genomes. Existing ...
  • The Origin and Evolution of the Ribosome
    Smith, Temple F; Lee, Jung C; Gutell, Robin R; Hartman, Hyman (BioMed Central, 2008-4-22)
    BACKGROUND. The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA interactions. Comparison between the ...
  • Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
    Shen, Yang; Paschalidis, Ioannis Ch.; Vakili, Pirooz; Vajda, Sandor (Public Library of Science, 2008-10-10)
    Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic ...
  • Survey of Human Mitochondrial Diseases Using New Genomic/Proteomic Tools
    Plasterer, Thomas N; Smith, Temple F; Mohr, Scott C (BioMed Central, 2001-06-01)
    BACKGROUND. We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein ...
  • Transcription Factor Map Alignment of Promoter Regions
    Blanco, Enrique; Messeguer, Xavier; Smith, Temple F; Guigó, Roderic (Public Library of Science, 2006-5-26)
    We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed ...

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