coli reshapes the in vivo mutational landscape of a model enzyme. Altered expression of a quality control protease in E. Thompson S, Zhang Y, Ingle C, Reynolds KA, Kortemme T.The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Expanding the space of protein geometries by computational design of de novo fold families. Pan X, Thompson M, Zhang Y, Lin L, Fraser JS, Kelly MJ, Kortemme T.New computational protein design methods for de novo small molecule binding sites. Glasgow A*, Glasgow J*, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ., Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Lim SA, Zhou XX, Hobman TC, Kortemme T, Wells JA. Engineered ACE2 receptor traps potently neutralize SARS-CoV-2.Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Recent advances in de novo protein design: principles, methods, and applications. Systems-level effects of allosteric perturbations to a model molecular switch. Perica T*, Mathy CJP*, Xu J, Jang GΜ, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJ S, Krogan NJ, Kortemme T.De novo protein fold families expand the designable ligand binding site space. Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Conchúir SO, Roy Burman S, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.Accurate positioning of functional residues with robotics-inspired computational protein design. Krivacic C*, Kundert K*, Pan X*, Pache RA*, Liu L, Conchúir SO, Jeliazkov JR, Gray JJ, Thompson MC, Fraser JS, & Kortemme T.Kretschmer S & Kortemme T. Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology.Complete mutational mapping of a GTPase switch in vivo reveals novel allosteric regulation. Mathy, CJP, Mishra P, Flynn JM, Perica T, Mavor D, Bolon DNA, & Kortemme T.Ligand-induced changes in dynamics mediate long-range allostery in the lac repressor. Glasgow A, Hobbs HT, Perry ZR, Marqusee S, Kortemme T.
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