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Baker Lab website soon to be searchable on Google!

For some reason, this website was not populating when any combination of “Baker” and “lab” was searched through Google. We hope to have remedied this, and I am using this post as a way to get Google to crawl faster (by adding new “content”). Thanks to everyone who has been notifying me of this issue. …

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Accurate de novo design of hyperstable constrained peptides

Small constrained peptides combine the stability of small molecule drugs with the selectivity and potency of antibody-based therapeutics. However, peptide-based therapeutics have largely remained underexplored due to the limited diversity of naturally occurring peptide scaffolds, and a lack of methods to design them rationally. In an article published in Nature this week, Baker lab scientists …

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The coming of age of de novo protein design

Most protein design efforts to date have focused on reengineering existing proteins found in nature.  By contrast, de novo protein design generates new structures from scratch, with sequences unrelated to naturally occurring proteins.  Before 2011, the only successful de novo designed proteins were Top7 (2003), and an array of coiled coil peptides (helical bundles).  In …

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Design of a hyperstable 60-subunit protein icosahedron

The icosahedron is the largest of the Platonic solids, and icosahedral protein structures are widely used in biological systems for packaging and transport1, 2. There has been considerable interest in repurposing such structures3, 4, 5 for applications ranging from targeted delivery to multivalent immunogen presentation. The ability to design proteins that self-assemble into precisely specified, …

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Determining large protein structures (>200 amino acids) from limited NMR data using Rosetta

Raman, Lange et al, Science, 327, 1014-8. (2010) Large protein structures can now be determined by incorporating backbone-only NMR data into Rosetta. Shown here is the structural comparison of ALG13 (201 amino acids) determined.(A) computationally using RDCs and backbone NH-NH NOEs. (B) experimentally by conventional NMR methods (PDB id : 2jzc) Nuclear Magnetic Resonance (NMR) is …

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Computational design and optimization of Kemp eliminases

Rothlisberger D., Khersonsky O. et al, Nature, 453, 164-6. (2008) Khersonsky O., Rothlisberger D. et al, J Mol Biol, 396(4), 1025-42. (2010) We  designed several enzymes that catalyze Kemp elimination, a model reaction for proton transfer from carbon. These enzymes utilize two catalytic motifs and enhance the reaction rate up to 105-fold with multiple turnovers.  …

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Structure prediction problems solved by Foldit players

Cooper, Khatib et al, Nature, 466, 756-60. (2010) Examples of blind structure prediction problems in which players were successfully able to improve structures. Native structures are shown in blue, starting puzzles in red, and top scoring Foldit predictions in green. (a) The red starting puzzle had a register shift and the top scoring green Foldit prediction …

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Exploitation of binding energy for catalysis and design

Thyme, Summer B., et all. Nature 461, 1300-4. (2009) The monomeric homing endonuclease I-AniI cleaves with high sequence specificity in the center of a 20 base-pair DNA target site, with the N-terminal domain of the enzyme making extensive binding interactions with the left (-) side of the target site and the similarly structured C-terminal domain …

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De novo computational design of retro-aldol enzymes

Jiang, Lin, Althoff Eric A. et al, Science, 319, 1387-91. (2008) Using new algorithms that employ hashing techniques to construct active sites for multi-step reactions, we designed retro-aldolases that employ four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a non-natural substrate. Designs that utilized an explicit water molecule to mediate …

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High Resolution Protein Structure Refinement

Qian B, Raman S, et al. Nature 450, 259-64. (2007) A longstanding problem in computational biology is the refinement of low resolution protein structure models to more atomic-level accurate structures. A related challenge is refining low-resolution NMR models to the quality of high-resolution structures. NMR is a valuable tool for determining protein structures, particularly because …

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