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Modeling Structures and Motions of Loops in Protein Molecules
Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA
Department of Computer Science, Rice University, Houston, TX 77005, USA
Department of Bioengineering, Rice University, Houston, TX 77005, USA
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.
Received: 26 December 2011; in revised form: 10 January 2012 / Accepted: 3 February 2012 / Published: 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
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Shehu, A.; Kavraki, L.E. Modeling Structures and Motions of Loops in Protein Molecules. Entropy 2012, 14, 252-290.
Shehu A, Kavraki LE. Modeling Structures and Motions of Loops in Protein Molecules. Entropy. 2012; 14(2):252-290.
Shehu, Amarda; Kavraki, Lydia E. 2012. "Modeling Structures and Motions of Loops in Protein Molecules." Entropy 14, no. 2: 252-290.