DOUGLAS LOWELL THEOBALD

Summary

Affiliation: Brandeis University
Country: USA

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi Accurate structural correlations from maximum likelihood superpositions
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
    PLoS Comput Biol 4:e43. 2008
  5. ncbi 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. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi 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
  10. ncbi 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

Research Grants

  1. Bayesian analysis of structural shape and conformation
    DOUGLAS LOWELL THEOBALD; Fiscal Year: 2010

Collaborators

  • LESLIE GRIFFITH
  • KyeongJin Kang
  • Rachel M Mitton-Fry
  • Stefan R Pulver
  • Elaine C Chang
  • Vincent C Panzano
  • Paul A Garrity
  • Deborah S Wuttke
  • Leslie W Glustrom
  • Emily M Anderson

Detail Information

Publications13

  1. ncbi 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...
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi Accurate structural correlations from maximum likelihood superpositions
    Douglas L Theobald
    Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
    PLoS Comput Biol 4:e43. 2008
    ....
  5. ncbi 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. ncbi 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
    ..AVAILABILITY: ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org...
  7. ncbi 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...
  8. ncbi 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...
  9. ncbi 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...
  10. ncbi 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...
  11. ncbi 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...
  12. ncbi 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...

Research Grants1

  1. Bayesian analysis of structural shape and conformation
    DOUGLAS LOWELL THEOBALD; Fiscal Year: 2010
    ....