Pocket Detection using Fpocket2 at Phyre2

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priya sharma

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Sep 3, 2021, 11:39:20 PMSep 3
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I have a query related to pocket detection at Phyre2.

The software indicates different residues as pocket residues, each time when you submit the same sequence.

In short, if single sequence is searched at Phyre2 several times, each time the pocket residue will differ.

examples with two Phyre IDs:
e8fa74196b5ae628
57bbe5e68e7cd6ac

Can anyone explain this?

 

Powell, Harold

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Nov 18, 2021, 8:34:54 AMNov 18
to Phyre
Unfortunately, it's so long since I looked at the google groups that your jobs have expired.

However, if you run Phyre2 with a gap of more than a few days between jobs, then the fold library will have been updated from the PDB (we do this every week), so the top hit may be from a different template (check the 7-character code that starts something like "c1abcA_" for the solutions you are looking at).

Otherwise I'd need to see a concrete example so that I can invesitgate.

Harry

priya sharma

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Nov 18, 2021, 2:33:29 PMNov 18
to harold...@imperial.ac.uk, Phyre
Thankyou for your email. I appreciate that you looked into the query. 

I observed the problem when I gave job at the same time as well. 

Initially, when I repeated my results after 15days, the results got updated. 

Still, to be cautious for my anysis, I searched the same protein with 5 different names one after the other, in 5 tabs on my browser, still I faced the same problem.

It would be helpful, if you could try it yourself with 2 or 3 random sequences and run it in 5 tabs simultaneously. I am not sure about other properties, but pocket residues will change.

I had myself observed this with 5 to 6 protein sequences.


Please keep me updated. 

Thanks,
Priya Sharma.

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Powell, Harold

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Nov 19, 2021, 10:21:22 AMNov 19
to Phyre
Hi Priya

You're absolutely right - I just ran three jobs and get slightly different residues in the pockets detected each time. I'll investigate and see if the problem is straightforward to fix.

Harry

Powell, Harold

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Nov 19, 2021, 11:45:19 AMNov 19
to Phyre
Hi Priya

I think I've sorted out this problem now - I've run several identical jobs and  get the same results for each of them, which is a good start!

If you try with your jobs again and you get the same problem, don't hesitate to get in touch again.

best wishes

Harry
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