If we superimpose the modeled structure with template structure, how much RMSD is acceptable?
The answer depends a lot on what system are you modeling. For proteins the xray resolution is usually in the 2-3.5 Angstrom range so the the rmsd to the template within this range (even backbone only) is often great. As Priyanka suggested, though, when evaluating protein models a number of other criteria have to be considered. I could imagine a model with higher deviation that is still useful and has some good features.
For ligand docking 2 Angstroms (heavy atoms rmsd of the ligand) is good, 1 Angstrom and less is great (basically exact).
The generally acceptable range of the RMSD when model is overlapped to template is 2 Å. But this rmsd cannot be considered as the only criteria for evaluation of the model constructed. Some deviations at times can be considered.
The answer depends a lot on what system are you modeling. For proteins the xray resolution is usually in the 2-3.5 Angstrom range so the the rmsd to the template within this range (even backbone only) is often great. As Priyanka suggested, though, when evaluating protein models a number of other criteria have to be considered. I could imagine a model with higher deviation that is still useful and has some good features.
For ligand docking 2 Angstroms (heavy atoms rmsd of the ligand) is good, 1 Angstrom and less is great (basically exact).
2.5 Angstrom for insilico model
3 Angstrom for X-ray
protein-protein docking 3 Angstrom
Protein-ligand docking 2.5 Angstrom
Please find the following links: 1- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057020/ 2-https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/resolution 3-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2286547/
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