Dear researchers,
Suppose if i have a database of protein sequences , and each sequence in it shares a sequence similarity of more than 50 % with a sequence for which crystal structure is already available in the PDB.
Is it likely that any sequence in the database would fold into a different structure despite having a homologue in PDB? Please help me understand which modelling method , Homology or Ab initio, one should go with and why? Would appreciate any help. Thanks in advance.
In case of homology modelling a template is used for the structure prediction. Ab intio gives you model which is not biased to a template. While homology modelling is doubted in terms of biasedness, Ab intio modelling is just a prediction. Hence none of them are good or bad. There are some servers which use combined approach for structure prediction. These servers (Phyre, ITASSER, etc) predicts structures of small stretches of amino acids and matches them as folds with the crystal structure of proteins which has highest identity and similarity. Hence combined approach is better.
Dear Swarup,
I agree with Federico and Sayan. In this case homology modeling should be prefered if there is good template available. 50% or more is likely to be a good template. Considering the coverage and identiity you can use homology modelling or combination of homology modelling and ab-initio.
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