IRES (Internal ribosome entry site) of Hepatitis A virus
Hi everybody,
I want to download nucleotide sequence of Hepatitis A virus internal ribosome entry site (IRES). Please suggest!
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Ram
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pradeep.pant25 •
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pradeep.pant25 •
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You have over a thousand options here. You can also find it in genbank entries like this one with a bit of googling.
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Devon Ryan
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did you try : http://www.ncbi.nlm.nih.gov/nuccore/?term=%22hepatitis+A+virus%22[ORGN]+IRES
Please always state your background/write a bio so we know where you're coming from. I'd also like to draw your attention to point 6 of http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202 - it always helps when you give us more details. Please help us help you better!
Thanks for your comment RamRS, I am M.Sc (chemistry).
I want to dock IRES of HAV (strain HM-175) with a drug molecule and I am not getting its structure in pdb format (may be not reported yet). So I thought to download its nucleotide sequence first and then by using online software I will predict its 3D structure in pdb format which is required for docking.
I wonder how good the ab initio predictions are in these circumstances. It's probably good to be pretty skeptical of any results you get from this.
I agree. From what I recall of the structural biology courses from college, you need a sequence homology of at least 70% to even remotely trust the structure predicted by a tool. But this was in 2008, I'm pretty sure tools have improved by leaps and bounds now.
It'd be interesting to find someone who actually works on ab initio predictions like this. I haven't touched this stuff in ages (well before 2008), so I honestly haven't a clue how good the tools are these days.
I have a friend that works on Rosetta. I remember him mentioning that more the known constraints (disulphide bonds, etc), faster the prediction - but that is quite obvious, isn't it? For some reason, I never got into structural protein bioinformatics.
Thanks for your suggestions. Would you like to add or modify docking protocol which I am using (as mentioned above).
The prerequisite for docking is a reliable structure. You might wanna think about docking strategies after you resolve the structure issues you have.