DOUGLAS LOWELL THEOBALD

Summary

Affiliation: Brandeis University
Country: USA

Publications

  1. pmc Expression, purification, and spectral tuning of RhoGC, a retinylidene/guanylyl cyclase fusion protein and optogenetics tool from the aquatic fungus Blastocladiella emersonii.
    Melissa M Trieu
    J Biol Chem 292:10379-10389. 2017
  2. pmc An empirical test of convergent evolution in rhodopsins
    Kristine A Mackin
    Department of Biochemistry, Brandeis University
    Mol Biol Evol 31:85-95. 2014
  3. pmc Optimal simultaneous superpositioning of multiple structures with missing data
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, MS009, Waltham, MA 02454, USA
    Bioinformatics 28:1972-9. 2012
  4. pmc On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
    Douglas L Theobald
    Biochemistry Department, Brandeis University, Waltham, MA 02454, USA
    Biol Direct 6:60. 2011
  5. pmc Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem
    Douglas L Theobald
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 103:18521-7. 2006
  6. pmc Accurate structural correlations from maximum likelihood superpositions
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
    PLoS Comput Biol 4:e43. 2008
  7. doi request reprint A formal test of the theory of universal common ancestry
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 01778, USA
    Nature 465:219-22. 2010
  8. pmc THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures
    Douglas L Theobald
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    Bioinformatics 22:2171-2. 2006
  9. pmc Divergent evolution within protein superfolds inferred from profile-based phylogenetics
    Douglas L Theobald
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado, Boulder, CO 80309 0215, USA
    J Mol Biol 354:722-37. 2005
  10. pmc Nucleic acid recognition by OB-fold proteins
    Douglas L Theobald
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309 0215, USA
    Annu Rev Biophys Biomol Struct 32:115-33. 2003

Collaborators

  • LESLIE GRIFFITH
  • Melissa M Trieu
  • Kristine A Mackin
  • KyeongJin Kang
  • Rachel M Mitton-Fry
  • Aaron E Ammerman
  • Daniel D Oprian
  • Robert R Birge
  • Erin L Devine
  • Lindsey B Lamarche
  • Jordan A Greco
  • Richard A Roy
  • Elaine C Chang
  • Vincent C Panzano
  • Paul A Garrity
  • Stefan R Pulver
  • Leslie W Glustrom
  • Deborah S Wuttke
  • Emily M Anderson

Detail Information

Publications15

  1. pmc Expression, purification, and spectral tuning of RhoGC, a retinylidene/guanylyl cyclase fusion protein and optogenetics tool from the aquatic fungus Blastocladiella emersonii.
    Melissa M Trieu
    J Biol Chem 292:10379-10389. 2017
    ..We anticipate that this expression/purification system and these RhoGC mutants will facilitate mechanistic and structural exploration of this important enzyme...
  2. pmc An empirical test of convergent evolution in rhodopsins
    Kristine A Mackin
    Department of Biochemistry, Brandeis University
    Mol Biol Evol 31:85-95. 2014
    ....
  3. pmc Optimal simultaneous superpositioning of multiple structures with missing data
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, MS009, Waltham, MA 02454, USA
    Bioinformatics 28:1972-9. 2012
    ..This practice is inefficient, as it ignores important data, and it fails to satisfy the common least-squares criterion. In the extreme, disregarding missing positions prohibits the calculation of a superposition altogether...
  4. pmc On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence
    Douglas L Theobald
    Biochemistry Department, Brandeis University, Waltham, MA 02454, USA
    Biol Direct 6:60. 2011
    ..The model selection tests prefer common ancestry for this artificial data set...
  5. pmc Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem
    Douglas L Theobald
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 103:18521-7. 2006
    ..Our analysis generalizes, simplifies, and extends results from previous discussions of the ML Procrustes problem. An iterative algorithm is presented for the simultaneous, numerical determination of the ML solutions...
  6. pmc Accurate structural correlations from maximum likelihood superpositions
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
    PLoS Comput Biol 4:e43. 2008
    ....
  7. doi request reprint A formal test of the theory of universal common ancestry
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 01778, USA
    Nature 465:219-22. 2010
    ..These results provide powerful statistical evidence corroborating the monophyly of all known life...
  8. pmc THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures
    Douglas L Theobald
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    Bioinformatics 22:2171-2. 2006
    ..THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble...
  9. pmc Divergent evolution within protein superfolds inferred from profile-based phylogenetics
    Douglas L Theobald
    Department of Chemistry and Biochemistry, UCB 215, University of Colorado, Boulder, CO 80309 0215, USA
    J Mol Biol 354:722-37. 2005
    ..This method extends phylogenetics into the challenging "twilight zone" of sequence similarity, providing the first objective resolution of deep evolutionary relationships among distant protein families...
  10. pmc Nucleic acid recognition by OB-fold proteins
    Douglas L Theobald
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309 0215, USA
    Annu Rev Biophys Biomol Struct 32:115-33. 2003
    ..Intriguingly, the observation of shared nucleic acid polarity may shed light on the longstanding question concerning OB-fold origins, indicating that it is unlikely that members of this family arose via convergent evolution...
  11. pmc Analysis of Drosophila TRPA1 reveals an ancient origin for human chemical nociception
    KyeongJin Kang
    National Center for Behavioral Genomics, Waltham, Massachusetts 02454, USA
    Nature 464:597-600. 2010
    ..We propose that human pain perception relies on an ancient chemical sensor conserved across approximately 500 million years of animal evolution...
  12. ncbi request reprint Prediction of multiple tandem OB-fold domains in telomere end-binding proteins Pot1 and Cdc13
    Douglas L Theobald
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
    Structure 12:1877-9. 2004
    ..This common usage of multiple, tandem OB-fold domains in telomeric end binding proteins extends the known evolutionary conservation of eukaryotic end-protection mechanisms...
  13. pmc Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes
    Douglas L Theobald
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    EMBO J 22:4314-24. 2003
    ..This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA...
  14. ncbi request reprint Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13
    Rachel M Mitton-Fry
    Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, CO 80309 0215 USA
    J Mol Biol 338:241-55. 2004
    ..The structure reported here provides a foundation for understanding the mechanism by which Cdc13 recognizes GT-rich heterogeneous sequences with both unusually strong affinity and high specificity...