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Journal of Chemical Physics / Volume 117 / Issue 9 / ARTICLES / Polymers, Biopolymers, and Complex Systems

J. Chem. Phys. 117, 4602 (2002); http://dx.doi.org/10.1063/1.1494417 (14 pages)

Statistical mechanical refinement of protein structure prediction schemes: Cumulant expansion approach

Michael P. Eastwood1, Corey Hardin2, Zaida Luthey-Schulten2, and Peter G. Wolynes1

1Department of Chemistry and Biochemistry, University of California, La Jolla, California 92093-0371
2Department of Chemistry, University of Illinois, Urbana, Illinois 61801

(Received 5 March 2002; accepted 24 May 2002)

We discuss how protein structure prediction schemes may be refined via a cumulant expansion approach using optimization criteria motivated by energy landscape ideas. The approach is advantageously combined with a free energy profile analysis based on multiple histogram sampling methods, which enables a quantitative assessment of the effects of refinement on the energy landscape to be made. The approach is widely applicable, but is illustrated here for a previously described prediction scheme intended for use in the absence of any known homology information. The relationship to previous optimization schemes is discussed. © 2002 American Institute of Physics.

© 2002 American Institute of Physics

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KEYWORDS and PACS

Keywords

proteins, statistical mechanics, molecular biophysics, molecular configurations, higher order statistics, optimisation

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.1494417

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

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    A. Kolinski, A. Godzik, and J. Skolnick, J. Chem. Phys. 98, 7420 (1993)JCPSA6000098000009007420000001.

    A. Liwo, C. Czaplewski, J. Pillardy, and H. A. Scheraga, J. Chem. Phys. 115, 2323 (2001)JCPSA6000115000005002323000001.

    J. M. Deutsch and T. Kurosky, Phys. Rev. E 56, 4553 (1997).

    Y. Xia and M. Levitt, J. Chem. Phys. 113, 9318 (2000)JCPSA6000113000020009318000001.

    G. Archontis and M. Karplus, J. Chem. Phys. 105, 11246 (1996)JCPSA6000105000024011246000001.

    R. W. Zwanzig, J. Chem. Phys. 22, 1420 (1954)JCPSA6000022000008001420000001.

    A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).

    X. Kong and C. L. Brooks III, J. Chem. Phys. 105, 2414 (1996)JCPSA6000105000006002414000001.


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