How to use swiss-mod to predict the secondary structure and 3D structure of a protein?
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 &quot;why not?&quot;
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.