Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information.
1XPA and 1D4U were used as templates for modelling hydra XPA in Swiss Model.
The distribution of the sequence identities associated with the structural templates used in modeling is shown in Figure 3. 60% of models are based on a template with a sequence identity greater than 30%, a common threshold for building reliable homology models.
The parameter K is the total number of templates in the model.
Thereby, the database may be useful to select suitable protein structural templates in order to model the more distantly related protein homologs/analogs using the comparative modeling methods.
Thus, such parametrized templates can be easily introduced in the template design modelling environment and they integrate seamlessly with the supervisory control framework.
Errors 3 5 are relatively infrequent when sequences with more than 40% identity to the templates are modeled; in such a case, approximately 90% of the main chain atoms are likely to be modeled with an RMS deviation of about 1 Å between template and target proteins; the structural differences are usually limited to loops and side chains [25] [27].
We developed a conceptual model of exceptions, a methodology for eliciting and modeling exceptions, and templates for modeling them in an extension of the Object-Process Methodology (OPM a system analysis and design methodology and language that uses a single graphical model for describing systems, including their timing exceptions, which has been shown to be an effective modeling methodology.
Furthermore, independently of the HLA-DR crystal structure used as template in homology modelling, a similar predicted 3D structure and trimeric quaternary architecture was obtained for sbMHC, with major deviations occurring only within the sea bass MHCIIα1 domain.
Using this fourth strand as a template we modeled in the sequence of the CaMKII R3 element in more than one sequence register, and carried out a series of short molecular dynamics simulations (∼100 ns each).
