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Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: jdbrown444 on September 02, 2014, 09:35:13 am

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Title: RNA Structures
Post by: jdbrown444 on September 02, 2014, 09:35:13 am
Hi Xiang-Jun,

I tried running the program on RNA structures with protein interactions and it seems to not be able to recognize the interactions. Is this program only meant for DNA complexes? I saw in the description that this is focused on DNA-protein structures but later on you mention it can characterize DNA/RNA-protein interactions. I apologize if i misunderstood. My computer programing background is very limited. Thank you in advance.
Title: Re: RNA Structures
Post by: xiangjun on September 02, 2014, 03:57:22 pm
Hi,

Thanks for your question regarding SNAP's applicability to RNA-protein structures. Yes, SNAP can be used for RNA-protein complexes as well as DNA-protein complexes, by specifying explicitly the --rna option. Given the complexities of nucleic-acids/proteins interactions, I've intended to start SNAP with DNA-protein structures. Since this question has been brought up several times (both in the Forum and privately), here is the response. Note that in the future, the --rna option may be removed from SNAP when the functionality becomes default.

Move functionality is being added to SNAP, and a new release is coming out soon. As always, please do not hesitate to ask any SNAP-related questions on the Forum.

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.