Does SPRING outcome only contain C-alpha?

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Louisl
Posts: 2
Joined: Sun Apr 25, 2021 5:40 am

Does SPRING outcome only contain C-alpha?

Post by Louisl »

Hello Zhang Lab Team,

I'm using SPRING to predict my PPIs, but I find that the outcome pdb file of SPRING only contains C-alpha.
Is that the result of SPRING by default? Is there any approach to get the structure with all the atoms of each residue?

Thanks for any information
xiaogenz
Posts: 14
Joined: Sun Apr 25, 2021 12:02 am

Re: Does SPRING outcome only contain C-alpha?

Post by xiaogenz »

Yes, you can use FASPR (https://zhanglab.dcmb.med.umich.edu/FASPR/) to quickly generate the side-chain of each protein chain independently.
Louisl
Posts: 2
Joined: Sun Apr 25, 2021 5:40 am

Re: Does SPRING outcome only contain C-alpha?

Post by Louisl »

It seems that FASPR is not used to deal with C-alpha traces, as it is mentioned in FASPR page:
(1) there should be no missing N, CA, C and O atoms in the main chain

But I have found the script to reconstruct full atom model in the download page of SPRING.
The url: https://zhanglab.dcmb.med.umich.edu/spr ... struct.zip

Thanks for the help!
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