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Why do I get more than one model? To see other biotech frequently asked questions,
please visit http://biotech.fyicenter.com/faq/
(Continued from previous question...) Why do I get more than one model? There are several models that the Robetta server produces when you submit a sequence. If Robetta determines that there is more than one domain (or if an ab initio portion of the sequence is too big to be modeled by the ab initio protocol), Robetta breaks up the query into putative domains and models each of them separately. After doing so, it assembles the models into one contiguous chain. This means you can examine your models either as a complete chain, or by clicking on the domain number in the Ginzu domain info box, you can examine the results for each individual domain. Within each domain, there are several models. In the case of ab initio predictions, the models are the cluster centers of the most populated clusters, with the exception of the last model, which is the lowest energy decoy that was not a member of the previously represented clusters. In the case of homology modeling predictions, the second model is the model produced by the default K*Sync alignment, with the first, third, fourth, and fifth selected from the decoy ensemble by various energy discrimination methods. In the case of twilight-zone reliability parent detections, the first 5 models are homology modeled, and models six-ten modeled using the de novo protocol. (Continued on next question...)
Other Frequently Asked Questions
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