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Modeling Structures and Motions of Loops in Protein Molecules

by Amarda Shehu 1,2,* and Lydia E. Kavraki 3,4,5,*
1
Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
2
Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA
3
Department of Computer Science, Rice University, Houston, TX 77005, USA
4
Department of Bioengineering, Rice University, Houston, TX 77005, USA
5
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
*
Authors to whom correspondence should be addressed.
Entropy 2012, 14(2), 252-290; https://doi.org/10.3390/e14020252
Received: 26 December 2011 / Revised: 10 January 2012 / Accepted: 3 February 2012 / Published: 13 February 2012
(This article belongs to the Special Issue Loop Entropy)
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. View Full-Text
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
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Shehu, A.; Kavraki, L.E. Modeling Structures and Motions of Loops in Protein Molecules. Entropy 2012, 14, 252-290.

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