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Invited Talk
Global Optimization Challenges in High Resolution Protein Structure Prediction
David Baker

Wed Dec 06 02:00 PM -- 02:00 PM (PST) @

I will discuss efforts towards transforming structural biology from a largely experimental science to a primarily computational science. Specifically, I will describe

(1) Significant progress in ab initio computation of the structures of small proteins from equence information alone. Using over 100,000 computers distributed around the world, and a physically realistic atomic level forcefield, we can predict structures to less than 2-3Å from the crystal tructure for a number of small proteins (Bradley et al, Science 2005; http://boinc.bakerlab.org/rosetta/rahtoppredictions.php ).

(2) The high accuracy prediction of structures of protein-protein complexes from the structures of the isolated proteins for cases where there are not significant conformational changes, and our progress in docking with backbone flexibility (Furman et al, Science 2005).

(3) The computer based design of novel highly specific endonucleases for targeted genomics applications such as gene therapy (Ashworth et al, Nature in press).

(4) The design of new protein folds and protein interactions, and ongoing efforts to computationally design catalysts for reactions not catalyzed by naturally occurring enzymes and a vaccine for HIV.

Author Information

David Baker (University of Washington)

Dr. Baker is a Professor of Biochemistry at the University of Washington, Seattle. He received his Ph.D. degree in biochemistry from the University of California, Berkeley, where he worked with Randy Schekman. His postdoctoral work in biochemistry and biophysics was done with David Agard at the University of California, San Francisco. Dr. Baker has received young investigator awards from the Packard Foundation, the National Science Foundation, and the Beckman Foundation; the Irving Sigal Young Investigator Award from the Protein Society; and the Overton Award from the International Society of Computational Biology. He is a recipient of the Feynman Prize from the Foresight Institute and the AAAS Newcomb Cleveland Prize, and was recently elected a member of the National Academy of Sciences. David Baker uses a combination of experimental and computational approaches to understand the basic principles underlying protein folding and protein-protein interactions. He is applying this knowledge to the prediction and design of macromolecular structures and interactions.

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