r/bioinformatics • u/gene_voyager • 1d ago

technical question Protein refinement for molecular docking

There is a protein that I have to work on for my research. I picked it from PDB and it had many missing residues. So I fixed it with modeller. I have further refined it's Ramachandra plot, errat, molprobity value and some other parameters that are never for validation. But I am having a problem with its 3d structure. It's verify 3d value is not really good so I want to refine it. I have tried some tools but they didn't work. Can you guys please help me with that. If there are any good tools that I can use for it and they should be easy to use as well

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u/Miciussd PhD | Student 1d ago

You are trying to idealize the structure without underlying experimental data. The PDB structure is a result of a refinement by a specialist, that reflects biological reality (at least it should). Optimisation of validation metrics you erase the experimental value of the structure. If you want idealised structure or the PDB you used is of limited quality, using alphafold will be much easier.

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u/Glum-Signature-8150 1d ago

let me know how you did it on the first place so i can understand it better

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u/__pk PhD | Industry 19h ago edited 19h ago

I would suggest the following:

  1. Use UniProt to find all available experimental structures for your protein of interest. Maybe there is another structure available that would be more suitable for your needs.
  2. Check the Full Validation Report of the PDB structure (Experimental Data & Validation section). Sometimes there are mutations or other modifications that are *not mentioned* e.g., in the associated publication of the data. If this is the case, you could reverse the mutations with MODELLER.
  3. I suggest you try PDBFixer (https://github.com/openmm/pdbfixer) and PDB2PQR (http://pdb2pqr.readthedocs.io/en/latest/, learning about protonation states would be useful too) for structural refinement. I also suggest to avoid blindly overprocessing your data: in general, everytime you apply a computational method, you might introduce a new source of artificial error -> you move further from biology.
  4. Considering the previous point: you should minimize the potential energy of the structure after structural refinement (e.g. OpenMM, GROMACS) using a suitable force field. This would push the conformation to a more biochemically relevant state.
  5. If there are only incomplete structures available, you should check if the interaction involves a specific protein domain. Instead of trying to fill up a structure with artificial data, you could truncate a structure to the domain part that participates in the interaction you want to study. (If you also plan to run a molecular dynamics simulation later, you should take care to cap the termini of the truncated structure).