Publications

Laboratory of Computational Protein Design

Find Anastassia Vorobieva's publications on Pubmed or on Google Scholar

2021

De novo design of transmembrane β barrels
Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D
Science, 371, eabc8182 (2021)
DOI: 10.1126/science.abc8182

Incorporation of sensing modalities into de novo designed fluorescence-activating proteins
Klima JC, Doyle LA, Daho Lee J, Rappleye M, Gagnon LA, Yen Lee M, Barros EP, Vorobieva AA, Dou J, Bremner S, Quon JS, Chow CM, Carter L, Mack DL, Amaro RE, Vaughan JC, Berndt A, Stoddard BL, Baker D
Nature Communications 12, 856 (2021)
DOI:10.1038/s41467-020-18911-w

2019

Improving the efficiency of ligand-binding protein design with molecular dynamics simulations
Barros EP, Schiffer JM, Vorobieva AA, Dou J, Baker D, Amaro RE
Journal of Chememical Theory and Computation, 15, 5703–5715 (2019)
DOI:10.1021/acs.jctc.9b00483

2018

Balancing specificity and promiscuity in enzyme evolution: multidimensional activity transitions in the alkaline phosphatase superfamily
van Loo B, Bayer CD, Fischer G, Jonas S, Valkov E, Mohamed MF, Vorobieva A, Dutruel C, Hyvonen M, Hollfelder F
Journal of the American Chemical Society, 141, 370-387 (2018)
DOI:10.1021/jacs.8b10290

De novo design of a fluorescence-activating β-barrel
Dou D*, Vorobieva AA*, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight G, Yen Lee M, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D
Nature, 561, 485-491 (2018)
DOI:10.1038/s41586-018-0509-0
*Co-first autors

2014

Escherichia coli D-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway
Vorobieva AA, Shahneawz Khan M, Soumillion P
Journal of Biological Chemistry, 289, 29086-29096 (2014)
DOI:10.1074/jbc.M114.595363