I want to get a series of enzyme-substrate binding pose in one step of my research, but I met some questions:
- My enzyme strutures lack of experimental structure information, and some of them can form into homo-n-mer, so which one should I choose? Monomer from Alphafold database or homo-complex strutcure from SWISS-MODEL?
Of course, it depends on the active pocket information, but what I only know is some substrate binding sites and active sites from UniProt(based on similarity)
So I used p2rank tool to predict pockets, and tried to determine active pocket based on these two information.
- So the monomer is better if the pocket is not in subunit interface, and homo-complex is better when the pocket is in subunit interface, right? But in some cases, the rigid local enzyme structure will mask the "real" pocket, since some key residue were not in the final result...
- And there is still a question, the protocol I followed said before docking, the predicted enzyme struture should be relaxed, but when I checked the structure quality by MolProbity, the relaxed struture showed higher molProbity score(lower is better) and much higher clash score, so which one should I trust? The relax protocol made struture better or worse?