Loop modeling: Difference between revisions

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==Non-Template Based Techniques==

There are three problems that arise when using a non-template based technique. First, there are constraints that limit the possibilities for local region modeling. One such constraint is that loop termini are required to end at the correct anchor position. Also, the [[Ramachandran plot| Ramachandran]] space cannot contain a backbone of [[dihedral angle]]s. Second, a modeling program has to use a set procedure. Some programs use the “spare parts” approach as mentioned above. Other programs use a ‘’[[wikt:Special:Search/de novo|de novo]]’’ approach that samples sterically feasible loop conformations and selects the best one. Third, determining the best model means that a scoring method must be created to compare the various conformations (Adhikari 2012).

==References==