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Designing repeat proteins: a modular approach to protein design.
Parmeggiani F, Huang PS. Parmeggiani F, et al. Curr Opin Struct Biol. 2017 Aug;45:116-123. doi: 10.1016/ Epub 2017 Mar 3. Curr Opin Struct Biol. 2017. PMID: 28267654 Review.
Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks.
Yeh CT, Brunette TJ, Baker D, McIntosh-Smith S, Parmeggiani F. Yeh CT, et al. J Struct Biol. 2018 Feb;201(2):100-107. doi: 10.1016/j.jsb.2017.09.001. Epub 2017 Sep 7. J Struct Biol. 2018. PMID: 28890160
De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.
Huang PS, Feldmeier K, Parmeggiani F, Velasco DAF, Höcker B, Baker D. Huang PS, et al. Nat Chem Biol. 2016 Jan;12(1):29-34. doi: 10.1038/nchembio.1966. Epub 2015 Nov 23. Nat Chem Biol. 2016. PMID: 26595462 Free PMC article.
Computationally Designed Armadillo Repeat Proteins for Modular Peptide Recognition.
Reichen C, Hansen S, Forzani C, Honegger A, Fleishman SJ, Zhou T, Parmeggiani F, Ernst P, Madhurantakam C, Ewald C, Mittl PRE, Zerbe O, Baker D, Caflisch A, Plückthun A. Reichen C, et al. J Mol Biol. 2016 Nov 6;428(22):4467-4489. doi: 10.1016/j.jmb.2016.09.012. Epub 2016 Sep 21. J Mol Biol. 2016. PMID: 27664438
Rational design of α-helical tandem repeat proteins with closed architectures.
Doyle L, Hallinan J, Bolduc J, Parmeggiani F, Baker D, Stoddard BL, Bradley P. Doyle L, et al. Nature. 2015 Dec 24;528(7583):585-8. doi: 10.1038/nature16191. Epub 2015 Dec 16. Nature. 2015. PMID: 26675735 Free PMC article.
Exploring the repeat protein universe through computational protein design.
Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. Brunette TJ, et al. Nature. 2015 Dec 24;528(7583):580-4. doi: 10.1038/nature16162. Epub 2015 Dec 16. Nature. 2015. PMID: 26675729 Free PMC article.
Control of repeat-protein curvature by computational protein design.
Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Park K, et al. Nat Struct Mol Biol. 2015 Feb;22(2):167-74. doi: 10.1038/nsmb.2938. Epub 2015 Jan 12. Nat Struct Mol Biol. 2015. PMID: 25580576 Free PMC article.
A general computational approach for repeat protein design.
Parmeggiani F, Huang PS, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J, Mao L, Janjua H, Montelione GT, Hunt J, Baker D. Parmeggiani F, et al. J Mol Biol. 2015 Jan 30;427(2):563-75. doi: 10.1016/j.jmb.2014.11.005. Epub 2014 Nov 14. J Mol Biol. 2015. PMID: 25451037 Free PMC article.
Designed Armadillo repeat proteins: library generation, characterization and selection of peptide binders with high specificity.
Varadamsetty G, Tremmel D, Hansen S, Parmeggiani F, Plückthun A. Varadamsetty G, et al. J Mol Biol. 2012 Nov 23;424(1-2):68-87. doi: 10.1016/j.jmb.2012.08.029. Epub 2012 Sep 14. J Mol Biol. 2012. PMID: 22985964
Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core.
Parmeggiani F, Pellarin R, Larsen AP, Varadamsetty G, Stumpp MT, Zerbe O, Caflisch A, Plückthun A. Parmeggiani F, et al. J Mol Biol. 2008 Mar 7;376(5):1282-304. doi: 10.1016/j.jmb.2007.12.014. Epub 2007 Dec 14. J Mol Biol. 2008. PMID: 18222472
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