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Abstract
Annual Review of Biophysics
Vol. 37: 289-316 (Volume publication date June 2008)
(doi:10.1146/annurev.biophys.37.092707.153558)
The Protein Folding Problem

Ken A. Dill,1,2 S. Banu Ozkan,3 M. Scott Shell,4 and Thomas R. Weikl5
1Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143 email:
2Graduate Group in Biophysics, University of California, San Francisco, California 94143
3Department of Physics, Arizona State University, Tempe, Arizona 85287; email:
4Department of Chemical Engineering, University of California, Santa Barbara, California 93106; email:
5Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, 14424 Potsdam, Germany; email:

The “protein folding problem” consists of three closely related puzzles: (a) What is the folding code? (b) What is the folding mechanism? (c) Can we predict the native structure of a protein from its amino acid sequence? Once regarded as a grand challenge, protein folding has seen great progress in recent years. Now, foldable proteins and nonbiological polymers are being designed routinely and moving toward successful applications. The structures of small proteins are now often well predicted by computer methods. And, there is now a testable explanation for how a protein can fold so quickly: A protein solves its large global optimization problem as a series of smaller local optimization problems, growing and assembling the native structure from peptide fragments, local structures first.

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Authors:
Ken A. Dill
S. Banu Ozkan
M. Scott Shell
Thomas R. Weikl
Keywords:
structure prediction
funnel energy landscapes
CASP
folding code
folding kinetics

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