Hello I'm trying to build 3D model for ALS2 (ALSIN) protein. The websites like SWISS-MODEL can't give proper model. Also, I can't use I-TASSER because the protein is longer than 1500 amino acids. Which software do you suggest to draw proper 3D model for this protein?
We keep going over this - on seemingly the same topics and seemingly with the same posters - and nothing changes.
The websites like SWISS-MODEL can't give proper model.
What does this mean exactly? It is difficult to provide advice before you tell us why SWISS-MODEL did not work for you. If this is a continuation of your previous question where you were trying to model something without a template, the answer is the same: modeling a protein - or part of it - without a homologous template can't be done reliably in most cases. This goes for any program, not just SWISS-MODEL. Modeling a large protein without a template is almost impossible to do reliably. Again, this goes for any program. To be clear, >1500 amino acids is considered large, which is why I-TASSER won't even humor us by attempting to model.
Two options that I would recommend, in order of my preference: 1) model only parts of the protein for which you have homologous templates, and forget about the rest; 2) find out about a domain organization of your protein, divide it accordingly, and submit individual domains (presumably smaller than 1500) to I-TASSER. This option will give you some result for everything, but don't expect magic for regions without homologous templates (which brings us back to my suggested option #1).
Template-free modelling has improved considerably in the last few years, but just submitting a 1500+ residue protein is unlikely to give a decent model. Consider splitting it up by predicted domains, or just modelling the part you are interested in.