Douglas Lowell Theobald, Ph.D. - Related 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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17 most relevant papers in past 60 days:
Year Citation  Score
2021 Lima I, Cino EA. Sequence similarity in 3D for comparison of protein families. Journal of Molecular Graphics & Modelling. 106: 107906. PMID 33848948 DOI: 10.1016/j.jmgm.2021.107906   
2021 Hu J, Zheng LL, Bai YS, Zhang KW, Yu DJ, Zhang GJ. Accurate prediction of protein-ATP binding residues using position-specific frequency matrix. Analytical Biochemistry. 626: 114241. PMID 33971164 DOI: 10.1016/j.ab.2021.114241   
2021 Park SH, Siddiqi H, Castro DV, De Angelis AA, Oom AL, Stoneham CA, Lewinski MK, Clark AE, Croker BA, Carlin AF, Guatelli J, Opella SJ. Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Plos Pathogens. 17: e1009519. PMID 34003853 DOI: 10.1371/journal.ppat.1009519   
2021 Rhys GG, Dawson WM, Beesley JL, Martin FJO, Brady RL, Thomson AR, Woolfson DN. How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues. Biomacromolecules. PMID 33881308 DOI: 10.1021/acs.biomac.1c00131   
2021 Christoffer C, Chen S, Bharadwaj V, Aderinwale T, Kumar V, Hormati M, Kihara D. LZerD webserver for pairwise and multiple protein-protein docking. Nucleic Acids Research. PMID 33963854 DOI: 10.1093/nar/gkab336   
2021 Ramirez-Mondragon CA, Nguyen ME, Milicaj J, Hassan BA, Tucci FJ, Muthyala R, Gao J, Taylor EA, Sham YY. Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics. International Journal of Molecular Sciences. 22. PMID 33924837 DOI: 10.3390/ijms22094619   
2021 Jain R, Muneeruddin K, Anderson J, Harms MJ, Shaffer SA, Matthews CR. A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33875592 DOI: 10.1073/pnas.2019571118   
2021 El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. The Journal of Chemical Physics. 154: 124201. PMID 33810651 DOI: 10.1063/5.0039969   
2021 Chakraborty T, Polley S, Sinha D, Seal S, Sinha D, Mitra SK, Hazra J, Sau K, Pal M, Sau S. Structurally distinct unfolding intermediates formed from a staphylococcal capsule-producing enzyme retained NADPH binding activity. Journal of Biomolecular Structure & Dynamics. 1-18. PMID 33977860 DOI: 10.1080/07391102.2021.1924269   
2021 Bianchetti L, Sinar D, Depenveiller C, Dejaegere A. Insights into mineralocorticoid receptor homodimerization from a combined molecular modeling and bioinformatics study. Proteins. PMID 33713045 DOI: 10.1002/prot.26073   
2021 Mitra A, Sarkar A, Szabó MR, Borics A. Correlated Motions of Conserved Polar Motifs Lay out a Plausible Mechanism of G Protein-Coupled Receptor Activation. Biomolecules. 11. PMID 33946214 DOI: 10.3390/biom11050670   
2021 Smith LJ, Green CW, Redfield C. The 'Shape-Shifter' Peptide from the Disulphide Isomerase PmScsC Shows Context-Dependent Conformational Preferences. Biomolecules. 11. PMID 33926076 DOI: 10.3390/biom11050642   
2021 Wiese JG, Shanmugaratnam S, Höcker B. Extension of a de novo TIM barrel with a rationally designed secondary structure element. Protein Science : a Publication of the Protein Society. 30: 982-989. PMID 33723882 DOI: 10.1002/pro.4064   
2021 Almeida BC, Kaczmarek JA, Figueiredo PR, Prather KLJ, Carvalho ATP. Transcription factor allosteric regulation through substrate coordination to zinc. Nar Genomics and Bioinformatics. 3: lqab033. PMID 33987533 DOI: 10.1093/nargab/lqab033   
2021 Rezaei Adariani S, Kazemein Jasemi NS, Bazgir F, Wittich C, Amin E, Seidel CAM, Dvorsky R, Ahmadian MR. A comprehensive analysis of RAS-effector interactions reveals interaction hotspots and new binding partners. The Journal of Biological Chemistry. 100626. PMID 33930461 DOI: 10.1016/j.jbc.2021.100626   
2021 Bhasin M, Varadarajan R. Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets. Frontiers in Molecular Biosciences. 8: 635425. PMID 33778004 DOI: 10.3389/fmolb.2021.635425   
2021 Helliwell JR. Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies. Acta Crystallographica. Section a, Foundations and Advances. 77: 173-185. PMID 33944796 DOI: 10.1107/S205327332100317X