Summer B. Thyme, Ph.D. - Publications

Biochemistry University of Washington, Seattle, Seattle, WA 
protein structure prediction

12 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
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Thyme SB, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/s41592-020-0848-2  1
2016 Thyme S, Song Y. Computational Design of DNA-Binding Proteins. Methods in Molecular Biology (Clifton, N.J.). 1414: 265-83. PMID 27094297 DOI: 10.1007/978-1-4939-3569-7_16  0.64
2014 Thyme SB, Song Y, Brunette TJ, Szeto MD, Kusak L, Bradley P, Baker D. Massively parallel determination and modeling of endonuclease substrate specificity. Nucleic Acids Research. 42: 13839-52. PMID 25389263 DOI: 10.1093/nar/gku1096  1
2014 Gagnon JA, Valen E, Thyme SB, Huang P, Ahkmetova L, Pauli A, Montague TG, Zimmerman S, Richter C, Schier AF. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. Plos One. 9: e98186. PMID 24873830 DOI: 10.1371/journal.pone.0098186  1
2014 Wang Y, Khan IF, Boissel S, Jarjour J, Pangallo J, Thyme S, Baker D, Scharenberg AM, Rawlings DJ. Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus. Nucleic Acids Research. 42: 6463-75. PMID 24682825 DOI: 10.1093/nar/gku224  1
2014 Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with rosetta Methods in Molecular Biology. 1123: 265-282. PMID 24510272 DOI: 10.1007/978-1-62703-968-0-17  1
2014 Thyme SB, Boissel SJ, Arshiya Quadri S, Nolan T, Baker DA, Park RU, Kusak L, Ashworth J, Baker D. Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Research. 42: 2564-76. PMID 24270794 DOI: 10.1093/nar/gkt1212  1
2014 Gagnon JA, Valen E, Thyme SB, Huang P, Ahkmetova L. Correction: Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs (PLoS ONE (2014) 9, 5 (e98186) DOI: 10.1371/journal.pone.0098186) Plos One. 9. DOI: 10.1371/journal.pone.0106396  1
2012 Thyme SB, Baker D, Bradley P. Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. Journal of Molecular Biology. 419: 255-74. PMID 22426128 DOI: 10.1016/j.jmb.2012.03.005  1
2011 Szeto MD, Boissel SJ, Baker D, Thyme SB. Mining endonuclease cleavage determinants in genomic sequence data. The Journal of Biological Chemistry. 286: 32617-27. PMID 21778233 DOI: 10.1074/jbc.M111.259572  1
2011 Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D, Monnat RJ, Burt A, Crisanti A. A synthetic homing endonuclease-based gene drive system in the human malaria mosquito. Nature. 473: 212-5. PMID 21508956 DOI: 10.1038/nature09937  1
2009 Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. Exploitation of binding energy for catalysis and design. Nature. 461: 1300-4. PMID 19865174 DOI: 10.1038/nature08508  1
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