I have protein sequence but from alphafold the confident is very low (orange) and from PSIPRED tool, there are some sequences that are in disordered. How do i rectify this issue to get a proper functional protein? clue is multi epitopes with linkers.
Dear Haslina Asis
Your question isn’t quite clear and could use more detail. However, if you’re looking for a way to relax or stabilize the protein structure, you might consider molecular dynamics simulations using tools like GROMACS.
What is the source of this protein? It may be unstructured without a partner protein or ligand, DNA or RNA. If you haven't looked yet, check in BLAST what it most closely resembles, if there are regions with known functions, etc.
I also dont understand your question. Your protein may be disordered, in whole or in parts, and still be a "proper functional" protein. Not all proteins form well defined 3D structures. About 30% of human proteins are at least partly disordered. So this may not an issue that need to be rectified, but just a feature of this specific protein.
Refine the structure with tools like I-TASSER or Rosetta. Use linker optimization for multi-epitopes. Run MD simulations for stabilization. Try Modeller or SWISS-MODEL for homology modeling.
All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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