IRES (Internal ribosome entry site) of Hepatitis A virus

Question

[pradeep.pant25]

Hi everybody,

I want to download nucleotide sequence of Hepatitis A virus internal ribosome entry site (IRES). Please suggest!

[Pierre Lindenbaum]

did you try : http://www.ncbi.nlm.nih.gov/nuccore/?term=%22hepatitis+A+virus%22[ORGN]+IRES

[Ram]

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!

[pradeep.pant25]

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.

[Devon Ryan]

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.

[Ram]

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.

[Devon Ryan]

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.

[Ram]

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.

[pradeep.pant25]

Thanks for your suggestions. Would you like to add or modify docking protocol which I am using (as mentioned above).

[Ram]

The prerequisite for docking is a reliable structure. You might wanna think about docking strategies after you resolve the structure issues you have.

Answer 1

[Devon Ryan]

You have over a thousand options here. You can also find it in genbank entries like this one with a bit of googling.