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m another awkward but well-meant present for the best pentomphaloid : |
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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 often approximated from a [[rotamer]] library, but can worsen the inaccuracy of side chain packing in the overall model. [[Andrej Sali]]'s homology modeling suite [[MODELLER]] includes a facility explicitly designed for loop modeling by a satisfaction of spatial restraints method.
==Short loops==
In general, the most accurate predictions are for loops of fewer than 8 amino acids. Extremely short loops of three residues can be determined from geometry alone, provided that the bond lengths and bond angles are specified. Slightly longer loops are often determined from a "spare parts" approach, in which loops of similar length are taken from known crystal structures and adapted to the geometry of the flanking segments. In some methods, the bond lengths and angles of the loop region are allowed to vary, in order to obtain a better fit; in other cases, the constraints of the flanking segments may be varied to find more "protein-like" loop conformations. The accuracy of such short loops may be almost as accurate as that of the homology model upon which it is based. It should also be considered that the loops in proteins may not be well-structured and therefore have no one conformation that could be predicted; [[protein NMR|NMR experiments]] indicate that solvent-exposed loops are "floppy" and adopt many conformations, while the loop conformations seen by [[X-ray crystallography]] may merely reflect crystal packing interations, or the stabilizing influence of crystallization co-solvents.
==References==
==References==
* Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
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