Do anyone have any detail experience on psipred web server?
I need help on this matter. I have a few unannotated protein sequences, for which I want to do functional annotation.
I have already uploaded 2 two protein sequences on psipred web server. Result for both of them came great, specially GO annotation. However, I don't find any good 3D structure for those proteins. (I am using i-tasser server for 3D structure).
How could I validate those results of psipred? Is there any other tools or articles that describe such procedure?
Help would be very much appreciated.
If there is no good template/crystal structure, you can't go for homology modeling (swiss-model server, modeller). In that case, you can predict structure by some ab initio (Robetta) or threading program, but most of the cases you can't be sure this is accurate structure. Biological systems may be different than just prediction using some computer programs without prior knowledge. You can use some structural validation programs such as (Whatcheck, ProSA, Ramachandran plot etc) though. But they doesn't validate the accurate folding pattern.
thanks for the answer.
As far as I know (please correct me if I am wrong), In i-tasser server, the c-value should be greater than (-2) to be considered as a least suitable model. however, I found -2.56 and -2.76 for two of my protein sequences.
Without 3D structure, how can I do functional annotation? will any domain or motif help?
Since, psipred predicts based on several physio-chemical data and motif as well as secondary structure of a protein, could validation of these function be enough?
c-score in i-tasser is just confidence score. Yes, according to the server, your predicted structure doesn't have good quality. But even you get 0.1 score, native structure may be different. Without crystal structure, best thing you can get up to this point. However, you can do some domain or motif analyses based on evolutionary conservation. You can also try PFP (http://kiharalab.org/web/pfp.php) or SVMProt (http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi) for function prediction.
I would suggest you to go for threading using FUGUE server. Based on the z-score given by it, you can download the best template and alignment. Use MODELLER to generate the 3D structure and check the output using verify-3D.
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