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'''Loop modeling''' is a problem in [[protein structure prediction]] requiring the prediction of the [[chemical conformation|conformations]] of [[loop (biochemistry)|loop]] regions in [[protein]]s without the use of a structural template. The problem arises often in [[homology modeling]], where the [[tertiary structure]] of an [[amino acid sequence]] is predicted based on a [[sequence alignment]] to a ''template'', or a second sequence whose structure is known. Because loops have highly variable sequences even within a given [[structural motif]] or [[protein folding|protein fold]], they often correspond to unaligned regions in sequence alignments; they also tend to be located at the [[solvent]]-exposed surface of [[globular protein]]s and thus are more conformationally flexible. Consequently, they often cannot be modeled using standard homology modeling techniques. More constrained versions of loop modeling are also used in the data fitting stages of solving a protein structure by [[X-ray crystallography]], because loops can correspond to regions of low [[electron density]] and are therefore difficult to resolve.
Regions of a structural model that were predicted by loop modeling tend to be much less accurate than regions that were predicted using template-based techniques. The extent of the inaccuracy increases with the number of [[amino acid]]s in the loop. The loop amino acids' [[side chain]]s [[dihedral angle]]s are
==References==
* Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
* Chung SY, Subbiah S. (1996.) A structural explanation for the twilight zone of protein sequence homology. Structure 4: 1123–27.
==External links==
* [http://alto.compbio.ucsf.edu/modloop//modloop.html MODLOOP], public server for access to MODELLER's loop modeling facility
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