do we need to perform refinement like homology modelling in ab initio prediction methods like trROSETTA or Alphafold .If it is required suggest some techniques?
Ab initio modelling is done without reliance on template information as opposed to homology modelling. This means the prediction methods rely on fundamental physical principles and energy-based algorithms to generate protein structure models from scratch.
Errors may arise during the prediction due to algorithms limitation among many others. Hence, the reason for structural refinement.
I would advise still doing structural refinement even if the structure prediction was done using alphaFold which is reputed for its high accuracy. Based on my experience, the refinement increases the accuracy a bit and you can confirm this by performing the Ramachandran plot analysis before and after refinement.
Can you please suggest some servers for the refinements of structures predicted by alphafold
You can use GalaxyRefine https://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE
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