The goals of David Baker's research group are to develop robust methods to accurately compute the structures of biological macromolecules and interactions, and to design and experimentally validate novel macromolecules with new and useful functions. Recent highlights include the computational design of novel enzymes catalyzing reactions not catalyzed by naturally occurring enzymes, the blind prediction of structures of small proteins with atomic level accuracy, and the enlisting of the computers and brain power of people around the world to bear on these problems through Rosetta@home and FoldIt.
DiMaio F, Terwilliger T, Read R, Wlodawar A, Baker D. 2011. Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization. Nature, in press.
Cooper S, Khatib F, Treuille A, Barbero J, Lee, J, Beenen M, Leaver-Fay A, Baker D, Popovic Z. 2010. Players, Foldit Predicting Protein Structures With a Multiplayer Online Game. Nature 466(7307):756-760.
Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot T, Eletsky A, Szyperski T, Kennedy M, Prestegard J, Montelione GT, Baker D. 2010. NMR Structure Determination for Larger Proteins Using Backbone-Only Data. Science 327(5968):1014-1018.
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, Clair JLS, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. 2010. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction Science 329(5989):309-313.
Thyme SB, Jarjour J, Takeuchi, R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D. 2009. Exploitation of Homing Endonuclease Binding Energy for Catalysis and Design. Nature 461(7268):1300.
Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, Dechancie J, Betker J, Baker, D. Kemp elimination catalysts by computational enzyme design. Nature 2008 May 8; 453, 190-195.
Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, Zanghellini A, Baker, D. De novo computational design of retro-aldol enzymes. Science 2008 Mar 7;319(5868):1387-91.
Watters AL, Deka P, Corrent C, Callender D, Varani G, Sosnick T, et al. The highly cooperative folding of small naturally occurring proteins is likely the result of natural selection. Cell. 2007 Feb;128(3):613-24.
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, et al. High-resolution structure prediction and the crystallographic phase problem. Nature. 2007 Nov;450(7167):259-U7.
Barth P, Schonbrun J, Baker D. Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences of the United States of America. 2007 Dec 18;104(51):20635.
Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 2007 Sep;104(37):14664-9.
Malmstrom L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker, D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. Plos Biology. 2007 Apr;5(4):758-68.
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Jr., Stoddard BL, Baker, D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 2006 Jun 1;441(7093):656-9.
Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005 Sep 16;309(5742):1868-71.
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005 Oct 28;310(5748):638-42
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science. 2003 Nov;302(5649):1364-8.