Hello, everyone:
Recently, I was trying to build 3D structure of one protein which has no crystal structure, I was wondering some questions.
First, what are the lowest threshold of sequence coverage and identity between the target sequence and the template for comparative Modeling?
Second, Dose Ab Initio Prediction can generate reliable results for a protein with no significant sequence identity to the known template?
Third, using the popular software Itasser, the parameters of result are as listed follows: C-score is -0.78, TM-score is 0.61+-0.14 and Exp. RMSD is 9.4+-4.6. The manual says that result with C-score greater than -1.5 is reliable. However, I find that the sequence coverage between my target sequence and the best test template is 12% and 31% respectively, Dose anyone can give some evaluation on the prediction? Can I use it in the published article?
Finally, can any one suggest pepeline of classical articles for prediction of 3D structure?
Thanks very much for any reply!
There are no universal cut-offs.
Anything that supports or challenges an existing idea or that stimulates the process of ideation and reasoning is worth sharing with the reader.
The word "popular" reminds me of an adage: "What is popular is wrong; what is wrong is popular."
actually the coverage is quite unacceptable, we usualy don't accept less than 35% of coverage so as it reflects enormous degree of virtuality to the model, which in turn makes it useless for further structural analysis, the RMSD is also discouraging, usually a homology search on pdb may provide you some good templates to start where you could direct your modelling server to try, trials would then provide you some acceptable model for energy, local geometry and stability measurements for quality estimation methods, the case may be quite difficult for transmemebrane proteins so it depends..
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