Question: Protein modelling of genes carrying mutations/deletions
gravatar for Deep Adhya
10 weeks ago by
Deep Adhya0
Deep Adhya0 wrote:

Dear Biostar community,

Is there any way to model a truncated protein with missing amino acid sequences (as a result of genomic deletions in exons) in-silico? If so, does anyone know of reliable web tools or software for this purpose? I would also be grateful, if anyone can direct me to published articles if any of this kind of work?

Thank you

Best wishes, Deep Adhya

protein modelling • 111 views
ADD COMMENTlink modified 10 weeks ago by Mensur Dlakic5.5k • written 10 weeks ago by Deep Adhya0

I would originally suggest the tools listed at the Protein Model Portal, but I now see that the group no longer has funding. However, they still provide links to certain websites where you can upload any protein sequence and have it modeled.


ADD REPLYlink written 10 weeks ago by Kevin Blighe60k
gravatar for Mensur Dlakic
10 weeks ago by
Mensur Dlakic5.5k
Mensur Dlakic5.5k wrote:

The answer to your question depends on your exact circumstances. If you have a homologous template, then the answer is yes. By this I mean that if there is a crystal structure of a similar protein that includes the part missing in yours, you will be able to model the deleted part. If there is no homologous structure, you will still be able to model it, but not in a reliable way. I suggest you check the links on the right side of this page and previous discussions here and here.

ADD COMMENTlink written 10 weeks ago by Mensur Dlakic5.5k

Thanks Mensur. My aim is to model a protein (eg NRXN1) without the deleted amino acid sequence of interest. I have found a couple of ab-initio protein modellers, the I-TASSER and Phyre2, and they appear to model the wild-type sequences quite accurately. I will try out the protein sequence with the delete sequences now, but there would be no way of knowing if they have been modelled reasonably accurately? Thanks

ADD REPLYlink written 9 weeks ago by Deep Adhya0
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