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Are there any issues with long sequences? To see other biotech frequently asked questions,
please visit http://biotech.fyicenter.com/faq/
(Continued from previous question...) Are there any issues with long sequences? The de novo protocol suffers, as do all such methods, from a limitation in the ability to sample conformations available to the protein. Larger targets that are high contact-order are more difficult to sample in a reasonable amount of computer time, and probably require much larger decoy ensembles than the Robetta server can afford to generate. Therefore, we impose a de novo domain size limit of about 200 residues, which is clearly often incorrect, but necessary. It is hoped that in such cases, features of the target are still captured by the models. There is additionally a limit on the length of the full chain of about 650 residues, so that the independently modeled domains may be assembled into a contiguous chain. (Continued on next question...)
Other Frequently Asked Questions
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