I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling.

I'm getting confused with how and when to use Jpred, swiss-mod, and PDB. So far, I got the sequence from scanprosite, put it into swiss-mod, but what next? When does jpred come in?

  • $\begingroup$ I've tried to provide a general answer, but could you provide more specifics about the type of protein you have, and why you want to model it. Why are you using swiss model and jpred? $\endgroup$ – James May 17 '15 at 13:45

3D structure.

Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what the SWISS-MODEL server does, and I think it automates the BLAST alignments from PDB). If there are no similar structures, you can resort to ab initio modelling if you have a reasonably straight forward globular domain, otherwise you might need to draw in additional expertise.

There are so many specific factors that need to be taken into account for a project like this. Depending on what the model will be used for, different questions are relevant.

Secondary structure.

You will need a few different secondary structure predictors to make it convincing and then you will need to check that your secondary consensus matches your 3D structure. If they don't match you need to think about "why not?"

If there is a difference it usually indicates that some 3D interaction is involved in the folding, so your 3D model usually trumps the sequence structure predictions, but do check your 3D structure against the secondary structure predictions.

Secondary structure prediction is more useful when a 3D structure is not available and modelling one is not an option.

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    $\begingroup$ Metaserver runs several methods for you and runs consensus analysis (and a bunch of other stuff). I'd start there. $\endgroup$ – Davidmh Jul 6 '15 at 3:54
  • $\begingroup$ That's a good one to start with, but ultimately will still be "trumped" by modelling (from a good alignment). $\endgroup$ – James Jul 6 '15 at 8:21

Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary structure prediction.

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  • $\begingroup$ So when i'm using Jpred, I get a bunch of 'hits' from pdb. what are these, just very similar sequences? $\endgroup$ – Ksims May 3 '15 at 3:33
  • $\begingroup$ Do those hits come with a score? $\endgroup$ – James May 17 '15 at 13:46

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