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Entropy 2012, 14(2), 252-290; doi:10.3390/e14020252
Review

Modeling Structures and Motions of Loops in Protein Molecules

1,2,*  and 3,4,5,*
Received: 26 December 2011; in revised form: 10 January 2012 / Accepted: 3 February 2012 / Published: 13 February 2012
(This article belongs to the Special Issue Loop Entropy)
Download PDF [3695 KB, uploaded 13 February 2012]
Abstract: Unlike the secondary structure elements that connect in protein structures, loop fragments in protein chains are often highly mobile even in generally stable proteins. The structural variability of loops is often at the center of a protein’s stability, folding, and even biological function. Loops are found to mediate important biological processes, such as signaling, protein-ligand binding, and protein-protein interactions. Modeling conformations of a loop under physiological conditions remains an open problem in computational biology. This article reviews computational research in loop modeling, highlighting progress and challenges. Important insight is obtained on potential directions for future research.
Keywords: loop modeling; conformational ensemble; equilibrium fluctuations; native state; structural analysis of proteins; structural bioinformatics loop modeling; conformational ensemble; equilibrium fluctuations; native state; structural analysis of proteins; structural bioinformatics
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Shehu, A.; Kavraki, L.E. Modeling Structures and Motions of Loops in Protein Molecules. Entropy 2012, 14, 252-290.

AMA Style

Shehu A, Kavraki LE. Modeling Structures and Motions of Loops in Protein Molecules. Entropy. 2012; 14(2):252-290.

Chicago/Turabian Style

Shehu, Amarda; Kavraki, Lydia E. 2012. "Modeling Structures and Motions of Loops in Protein Molecules." Entropy 14, no. 2: 252-290.


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