There are many membrane proteins with more than 1200 amino acids.Please inform me about a protocol for modeling and after modeling how can I validate it.
You can try SWISS-MODEL that is easy to use . it is an automated protein structure homology-modelling server accessible via the ExPASy web server. You need to have a software to visualize like Pymol.
I assume you have the concerned FASTA sequence at hand. Using the FASTA sequence(s) you can generate PDB files using SWISS-MODEL Workspace. [ Keep in mind that you would be needing a template]. Once you have your homology model, you can validate the predicted structure by checking up the Ramachandran Plot analysis. Feed in your .PDB file into MOLPROBITY and analyze the conformational geometry of your modelled protein.
Use a homology modelling server (I recommend IntFOLD or iTASSER). Load your protein fasta sequence into the server and run (it will take several hours). By choosing to thread your sequence onto a specified template you bias your output and may not generate a biologically-relevant structure.
Homology modelling servers will use specified criteria (sequence similarity at a global and local level) to select the most suitable structure(s) to use as a basis for the prediction and produce the predicted structure and are therefore less biased than one you choose yourself (unless of course your protein has high sequence similarity to a known structure).
Validation can take 3 forms. Firstly look at the chemistry of the protein- are there surface-exposed hydrophobic residues at predicted transmembrane regions etc.
Then look at the functionality of the protein. Are catalytically important residues in the right place? Does your structure make sense in terms of mutants known to disrupt function?
Finally (and most importantly), can you make meaningful, testable hypotheses using this structure? Look at residues that might be important for function, mutate them and look at the effect- the exact same way you validate an experimentally-derived structure.
You should give some more details about your protein, for instance what is the oligomeric form of the functional unit of your protein?? 1500 amino acid residues constitute the monomer or the oligomer?? You may refer to our recent papers: