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Douglas Lowell Theobald, Ph.D. - Publications

Affiliations: 
2007- Biochemistry Brandeis University, Waltham, MA, United States 
Area:
Telomeres, molecular evolution, structural bioinformatics, superposition, rhodopsin, bacteriorhodopsin, lactate dehydrogenase, malate dehydrogenase
Website:
http://theobald.brandeis.edu/
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Kumar RP, Matos JO, Black BY, Ellenburg WH, Chen J, Patterson M, Gehtman JA, Theobald DL, Krauss IJ, Oprian DD. Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction. Biorxiv : the Preprint Server For Biology. PMID 38746203 DOI: 10.1101/2024.05.04.592530  0.762
2024 Frank HM, Walujkar S, Walsh RM, Laursen WJ, Theobald DL, Garrity PA, Gaudet R. Structural basis of ligand specificity and channel activation in an insect gustatory receptor. Cell Reports. 43: 114035. PMID 38573859 DOI: 10.1016/j.celrep.2024.114035  0.638
2023 Frank HM, Walujkar S, Walsh RM, Laursen WJ, Theobald DL, Garrity PA, Gaudet R. Structure of an insect gustatory receptor. Biorxiv : the Preprint Server For Biology. PMID 38187590 DOI: 10.1101/2023.12.19.572336  0.639
2022 Ordabayev YA, Friedman LJ, Gelles J, Theobald DL. Bayesian machine learning analysis of single-molecule fluorescence colocalization images. Elife. 11. PMID 35319463 DOI: 10.7554/eLife.73860  0.514
2022 Stiller JB, Otten R, Häussinger D, Rieder PS, Theobald DL, Kern D. Structure determination of high-energy states in a dynamic protein ensemble. Nature. 603: 528-535. PMID 35236984 DOI: 10.1038/s41586-022-04468-9  0.512
2021 Norn C, André I, Theobald DL. A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices. Protein Science : a Publication of the Protein Society. PMID 34218472 DOI: 10.1002/pro.4155  0.753
2019 Moreta LS, Al-Sibahi AS, Theobald D, Bullock W, Rommes BN, Manoukian A, Hamelryck T. A Probabilistic Programming Approach to Protein Structure Superposition. Proceedings of the ... Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology : Cibcb. Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology. 2019. PMID 34661202 DOI: 10.1109/cibcb.2019.8791469  0.78
2018 Wirth JD, Boucher JI, Jacobowitz JR, Classen S, Theobald DL. Functional and Structural Resilience of the Active Site Loop in the Evolution of Plasmodium Lactate Dehydrogenase. Biochemistry. PMID 30358994 DOI: 10.1021/Acs.Biochem.8B00913  0.762
2017 Lamarche LB, Kumar RP, Trieu MM, Devine EL, Theobald DL, Oprian DD. Purification and Characterization of RhoPDE, a Retinylidene/Phosphodiesterase Fusion Protein and Potential Optogenetics Tool from the Choanoflagellate Salpingoeca rosetta. Biochemistry. PMID 28976747 DOI: 10.1021/Acs.Biochem.7B00519  0.804
2017 Trieu MM, Devine EL, Lamarche LB, Ammerman AE, Greco JA, Birge RR, Theobald DL, Oprian DD. Expression, Purification, and Spectral Tuning of RhoGC, a Retinylidene/Guanylyl Cyclase Fusion Protein and Optogenetics Tool from the Aquatic Fungus Blastocladiella emersonii. The Journal of Biological Chemistry. PMID 28473465 DOI: 10.1074/Jbc.M117.789636  0.785
2016 Nguyen V, Wilson C, Hoemberger M, Stiller JB, Agafonov RV, Kutter S, English J, Theobald DL, Kern D. Evolutionary drivers of thermoadaptation in enzyme catalysis. Science (New York, N.Y.). PMID 28008087 DOI: 10.1126/Science.Aah3717  0.571
2016 Devine EL, Theobald DL, Oprian DD. Relocating the active-site lysine in rhodopsin: 2. Evolutionary intermediates. Biochemistry. PMID 27486845 DOI: 10.1021/Acs.Biochem.6B00478  0.804
2016 Theobald DL. Presenilin adopts the ClC channel fold. Protein Science : a Publication of the Protein Society. PMID 26971579 DOI: 10.1002/Pro.2919  0.332
2016 Steindel PA, Chen EH, Wirth JD, Theobald DL. Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases. Protein Science : a Publication of the Protein Society. PMID 26889885 DOI: 10.1002/Pro.2904  0.799
2015 Wilson C, Agafonov RV, Hoemberger M, Kutter S, Zorba A, Halpin J, Buosi V, Otten R, Waterman D, Theobald DL, Kern D. Kinase dynamics. Using ancient protein kinases to unravel a modern cancer drug's mechanism. Science (New York, N.Y.). 347: 882-6. PMID 25700521 DOI: 10.1126/Science.Aaa1823  0.576
2014 Boucher JI, Jacobowitz JR, Beckett BC, Classen S, Theobald DL. An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases. Elife. 3. PMID 24966208 DOI: 10.7554/Elife.02304  0.747
2014 Mackin KA, Roy RA, Theobald DL. An empirical test of convergent evolution in rhodopsins. Molecular Biology and Evolution. 31: 85-95. PMID 24077848 DOI: 10.1093/Molbev/Mst171  0.768
2014 Boucher JI, Jacobowitz JR, Beckett BC, Classen S, Theobald DL. Author response: An atomic-resolution view of neofunctionalization in the evolution of apicomplexan lactate dehydrogenases Elife. DOI: 10.7554/Elife.02304.036  0.689
2013 Mardia KV, Fallaize CJ, Barber S, Jackson RM, Theobald DL. BAYESIAN ALIGNMENT OF SIMILARITY SHAPES. The Annals of Applied Statistics. 7: 989-1009. PMID 24052809 DOI: 10.1214/12-Aoas615  0.552
2013 Ni L, Bronk P, Chang EC, Lowell AM, Flam JO, Panzano VC, Theobald DL, Griffith LC, Garrity PA. A gustatory receptor paralogue controls rapid warmth avoidance in Drosophila. Nature. 500: 580-4. PMID 23925112 DOI: 10.1038/Nature12390  0.633
2013 Devine EL, Oprian DD, Theobald DL. Relocating the active-site lysine in rhodopsin and implications for evolution of retinylidene proteins. Proceedings of the National Academy of Sciences of the United States of America. 110: 13351-5. PMID 23904486 DOI: 10.1073/Pnas.1306826110  0.809
2013 Lyumkis D, Brilot AF, Theobald DL, Grigorieff N. Likelihood-based classification of cryo-EM images using FREALIGN. Journal of Structural Biology. 183: 377-88. PMID 23872434 DOI: 10.1016/J.Jsb.2013.07.005  0.549
2012 Theobald DL, Steindel PA. Optimal simultaneous superpositioning of multiple structures with missing data. Bioinformatics (Oxford, England). 28: 1972-9. PMID 22543369 DOI: 10.1093/Bioinformatics/Bts243  0.771
2011 Theobald DL. On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence. Biology Direct. 6: 60. PMID 22114984 DOI: 10.1186/1745-6150-6-60  0.377
2011 Piasta KN, Theobald DL, Miller C. Potassium-selective block of barium permeation through single KcsA channels. The Journal of General Physiology. 138: 421-36. PMID 21911483 DOI: 10.1085/Jgp.201110684  0.769
2011 Liu P, Agrafiotis DK, Theobald DL. Rapid communication reply to comment on: "Fast determination of the optimal rotational matrix for macromolecular superpositions" Journal of Computational Chemistry. 32: 185-186. DOI: 10.1002/Jcc.21606  0.353
2010 Kang K, Pulver SR, Panzano VC, Chang EC, Griffith LC, Theobald DL, Garrity PA. Analysis of Drosophila TRPA1 reveals an ancient origin for human chemical nociception. Nature. 464: 597-600. PMID 20237474 DOI: 10.1038/Nature08848  0.623
2010 Theobald DL, Miller C. Membrane transport proteins: surprises in structural sameness. Nature Structural & Molecular Biology. 17: 2-3. PMID 20051980 DOI: 10.1038/Nsmb0110-2  0.514
2010 Steindel P, Theobald D. Analysis of Nucleic Acid Conformations and Amino Acid Propensities in Single-Stranded Binding Proteins Biophysical Journal. 98: 270a. DOI: 10.1016/J.Bpj.2009.12.1471  0.776
2008 Theobald DL, Wuttke DS. Accurate structural correlations from maximum likelihood superpositions. Plos Computational Biology. 4: e43. PMID 18282091 DOI: 10.1371/Journal.Pcbi.0040043  0.667
2006 Theobald DL, Wuttke DS. Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem. Proceedings of the National Academy of Sciences of the United States of America. 103: 18521-7. PMID 17130458 DOI: 10.1073/Pnas.0508445103  0.589
2006 Theobald DL, Wuttke DS. THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics (Oxford, England). 22: 2171-2. PMID 16777907 DOI: 10.1093/Bioinformatics/Btl332  0.649
2005 Theobald DL, Wuttke DS. Divergent evolution within protein superfolds inferred from profile-based phylogenetics. Journal of Molecular Biology. 354: 722-37. PMID 16266719 DOI: 10.1016/J.Jmb.2005.08.071  0.681
2004 Theobald DL, Wuttke DS. Prediction of multiple tandem OB-fold domains in telomere end-binding proteins Pot1 and Cdc13. Structure (London, England : 1993). 12: 1877-9. PMID 15458635 DOI: 10.1016/J.Str.2004.07.015  0.66
2004 Mitton-Fry RM, Anderson EM, Theobald DL, Glustrom LW, Wuttke DS. Structural basis for telomeric single-stranded DNA recognition by yeast Cdc13. Journal of Molecular Biology. 338: 241-55. PMID 15066429 DOI: 10.1016/J.Jmb.2004.01.063  0.788
2003 Theobald DL, Cervantes RB, Lundblad V, Wuttke DS. Homology among telomeric end-protection proteins. Structure (London, England : 1993). 11: 1049-50. PMID 12962623 DOI: 10.1016/S0969-2126(03)00183-7  0.661
2003 Theobald DL, Schultz SC. Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes. The Embo Journal. 22: 4314-24. PMID 12912928 DOI: 10.1093/Emboj/Cdg415  0.72
2003 Theobald DL, Mitton-Fry RM, Wuttke DS. Nucleic acid recognition by OB-fold proteins. Annual Review of Biophysics and Biomolecular Structure. 32: 115-33. PMID 12598368 DOI: 10.1146/Annurev.Biophys.32.110601.142506  0.79
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