<< model quality for docking >>

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I. Camps

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Nov 25, 2015, 6:40:39 AM11/25/15
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Hello,

I have been working with molecular docking for a while.

Til now, I always be lucky enough to get the structures from Protein Data Bank :)

Now, I am working with some proteins (from fungi) that there aren't X-Ray structures. So, I search for a reliable tool to predict structures and found Phyre.

In my first job (42b752f1abbc2514), the alignment covering is 21% whereas the confidence is 96% and the percentage identity is 17%.

My doubt: what criterion should I use to select a model and use it in my docking studies?

Regards,

Camps

hugo jesus Valdivia

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Nov 25, 2015, 10:03:04 AM11/25/15
to ica...@gmail.com, Phyre
Hi Mr. Camps

Maybe this tutorial can help you.

BW,

HV

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kelley2015.pdf

Saurabh Gayali

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Sep 24, 2019, 1:47:54 AM9/24/19
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@ hugo jesus valdivia
I don't think the attachment is a tutorial. It is the article for Phyre.

@ I. Camps

I am also trying to acheive something similar. I will use the predicted structures above 90% confidence.

 
It is not recommended to consider models with a confidence value of <90%.
 
-according to the Phyre publication.
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