hi, i am seeking for a tool or method for making protein prediction for a rare sequence, the protein has 256 residues and doesn't have any template which aligns, also there are 34 Gly, 10 Pro residue at the first 1-100 residue. Thus, the tools such as swiss, itasser, phyre.. can not predict approximately first 1-120 res, i wonder if is there any tool or method to overcome the trouble
You can use some de novo prediction tools like rosetta or quark but it can take you some time to do that, and the accuracy may be a problem.
Jorgaq Pata, thank you for your answer.
I got some models from quark in two days but it seems there isn't any criteria to compare of the quality of selected model. Let me try to rosetta then make cross rank, thanks a lot
You can try ITASSER suite, it is one of the best protein modelling servers available, you can try energy minimization later on. Try using SWISS PDB Viewer or CABS-FLEX sever for enerzyminizatio/simulation. Hope this helps.
Best Wishes,
Pankaj
Some sequences result in intrinsically disordered proteins. This may well be one of them. There is nothing to be gained in predicting the structure of something which is disordered in vivo
Pankaj Kumar Singh, Thanks for answer.
I tried both for prediction step, results are the same with template-required tools, and also will take into consideration your recommendaditons for the next step.
Thanks a lot.
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