Messages

1

RNA structures (DSSR) / Re: Can 3DNA be used to build a miRNA-target structure?

« on: November 22, 2012, 06:56:09 am »

Thank for your tips.
Your solution is the most practical to solve my challenge considering that i don't need of precise and minimized structure as initial input for my docking calculations.
Best regards

2

RNA structures (DSSR) / Re: Can 3DNA be used to build a miRNA-target structure?

« on: November 21, 2012, 11:29:36 am »

The empty spaces in alignment are mismatches


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3

RNA structures (DSSR) / Re: Can 3DNA be used to build a miRNA-target structure?

« on: November 21, 2012, 11:26:59 am »

Of course 
I ought to perform some docking studies on a experimentally validated (luciferase assay) pair mirna-target.
According to the assay, I can't determine the portion of the target that is bound by the mirna. Therefore I ran a mirna binding-site predictor on the mrna sequence of the target highlighting some interesting candidate positions. 
In order to further characterize my binding i thought to perform some dockings between the complex formed by mirna with the portion of target highlighted by predictors  and the Argonaute protein.
The central point is that i need to rebuild the pair mirna- target as highlighted by my predictors in order to use it as input for docking.
Here is an example  with part of the 2 sequences. The first sequence is the mirna and the second is the target


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I hope that my explanation is enough clear and sorry for the "naif" representation of the mirna-target pairment
Thank you very much
Guido Leoni

4

RNA structures (DSSR) / Can 3DNA be used to build a miRNA-target structure?

« on: November 21, 2012, 03:10:21 am »

Thank for your work with 3DNA.
Might it be possible to reproduce with 3DNA a structure of a mirna target pairment?
Best regards