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Published online before print December 22, 2006
Protein Science, DOI: 10.1110/ps.062270707
 Copyright © 2006 The Protein Society
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Prediction of structures of multidomain proteins from structures of the individual domains

Andrew M. Wollacott1,3, Alexandre Zanghellini1,2,3, Paul Murphy1, and David Baker1

1 Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
2 Biomolecular Structure and Design, University of Washington, Seattle, Washington 98195, USA

(RECEIVED April 7, 2006; FINAL REVISION October 30, 2006; ACCEPTED October 31, 2006)

We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low-resolution search in which the conformational space of the domain linker is explored using the Rosetta de novo structure prediction method, followed by a high-resolution search in which all atoms are treated explicitly and backbone and side chain degrees of freedom are simultaneously optimized. The method recapitulates, often with very high accuracy, the structures of existing multidomain proteins.

Keywords: domain assembly; protein–protein docking; protein structure prediction

3 These authors contributed equally to this work.

Reprint requests to: David Baker, Department of Biochemistry Health Sciences Building, Box 357350, Seattle, WA 98195, USA; e-mail: dabaker{at}u.washington.edu; fax: (206) 685-1792.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.062270707.

Abbreviations: RMSD, root mean square deviation.


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Copyright © 2006 by The Protein Society.