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Prediction of structures of multidomain proteins from structures of the individual domains

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

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