We are working on a multi-domain protein, and we need a three-dimensional structure. Although we used SWISS-MODEL to predict the structure, it did not give us a reliable structure. We also used I-TASSER to predict the structure of each domain separately. Is there a better tool to show the three-dimensional structure of this protein in general? Moreover, does it make sense to extract the three-dimensional structures of each second separately and combine them? In the sense that although the structure of each is clear, they create different foldings together.
Footnote, The protein structure in question, has about 2400 residues; most servers accept the FASTA format below 1500.
Yes, to predict such a large protein in one go is generally not possible, as these are usually too hard to crystallise, although more recently, cryo-EM has made large proteins more accessible .
First determine the domain organisation and identify segments that may be intrinsically disordered, or others that may be fibrillar rather than globular in structure. Then try to predict the individual domains - if you carefully look at the potential templates for the individual domains, you may find some which also show interaction with other domains that you can use to assemble larger parts of the protein. Intrinsically disordered segments will be flexible in the native protein, and may give you an idea what parts of your protein probably are flexible.
@Erfan Zaker
I am also facing a similar problem. I have already modeled the domains separately.
I am planning to use DEMO server (Zhang Lab) to assemble the domains and see the result. I have tried to assemble the full-length model using MODELLER 10.1 but I didn't get a correct model (out of 20 models generated).
I hope you also update the discussion should you found a useful solution.
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