A good validation score only tells you that the model is geometrically plausible. It does not tell you whether or not it is correct.
MJC answer is correct. Perhaps if the identities/similarities are concentrated in the recognition site (usually is) it s more relevant for docking
Matthew James Conroy gave a great answer, as did Mario Antonio Bianchet. The thing that you have to accept here is that even if your validation score is great it means that your predicted model is sterically allowed. It does not guarantee that your homology model is the real deal. Perhaps you could work with a different template and may be try SWISS PROTEIN Workspace to generate your .PDB files? If you have any literature on the predicted docking sites, may be you could try working with only that domain and not the full protein? Try looking up a good template for that domain?
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