Question: I need an explanation about Rosetta de novo structure prediction and fragments picking
gravatar for Palming
2.6 years ago by
Palming10 wrote:

Hello everyone,

I am currently trying to work with Rosetta. I have a peptide sequence and I would like to predict its structure using de novo structure prediction. I have Rosetta installed and I need to do this with Rosetta (so please, do not suggest any webservice such as Robetta). I tried following the Rosetta documentation: the de novo structure prediction tutorial states that required input files are the sequence in the fasta format and 9mer & 3mer fragments files. To obtain the fragment files, the turorial states:

There are multiple ways to obtain those fragment files. You can generate them on your local machine. For that to work you need additional software installed. How to do that is explained in a separate tutorial for fragment picking.

However, the fragment picking tutorial says you need three input files to generate fragments: the fasta sequence (which I have) ; the psipred .Ss2 file (which I have) and the structure (which, of course, I don't have). I have tried running the script for fragments picking: it works well when an input structure is given, but it doesn't work if there is no structure.

Therefore, here is my question: how can I do an ab initio structure prediction if I need fragment files whose generation requires a structure ? How do I generate fragments if I don't have a structure ? Or how do I do ab initio structure prediction if I don't have fragments ?

I am fairly new to Rosetta and the concept of fragments, so if I am missing something basic please tell me.

ADD COMMENTlink modified 19 months ago by shahram.mesdaghi0 • written 2.6 years ago by Palming10

Hi I have the same problems as you had. So how did you 'generate a fragment library from all available structures'? Thank you!

ADD REPLYlink written 19 months ago by shahram.mesdaghi0
gravatar for Palming
2.2 years ago by
Palming10 wrote:

If anyone is ever interested, I finally got the answer to my question :

Contrary to what h.mon suggested, you are not supposed to make a homology (or threading) model of your protein, then generate fragments from this model, and then use these fragments to make an ab initio model in Rosetta.

You are supposed to generate a fragment library from all available structures in databanks (e.g. from the PDB) and then generate your ab initio model. Which makes more sense.

Feel free to correct me if I'm wrong, or to add any relevant information for future reference.

ADD COMMENTlink written 2.2 years ago by Palming10

How did you generate a fragment library from all available structures in databanks?

ADD REPLYlink written 13 months ago by dokto20m0
gravatar for h.mon
2.6 years ago by
h.mon30k wrote:

You can obtain a pdb model if you check the BioSerf option at the PSIPRED server.

BioSerf Output

If you provide a valid MODELLER key you will have been able to run a BioSerf job. BioSerf is a fully automated homology modelling service which integrates PSI-BLAST, HHBlits, PSIPRED, GenTHREADER and MODELLER. The final output is a PDB file which can be viewed by clicking the BioSerf tab on the results page.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by h.mon30k

Thank you for your answer. What doesn't make sense to me is generating fragments from a model. If I make fragments from a homology model, then the ab initio model will highly depend on the quality of the original model, won't it ? In that case, why even bother making an ab initio model ? Can it be better than the homology model the fragments are based on ?

ADD REPLYlink written 2.6 years ago by Palming10
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