My software notes

February 14, 2012

[web server] RNA Frabase 2.0

Filed under: servers — kpwu @ 8:48 pm

My colleague asked me to know if I can generate/model 3D structure of a short, single chain RNA. I know there are some servers doing such task but I am not sure how reliable the de novo structures are.

Instead of de novo structure model, I found there is a nice website called “RNA Frabase 2.0” (http://rnafrabase.ibch.poznan.pl/) which provides easy-to-use interface.

For example, I put a short RNA sequence “UAUUC” to search the published RNA structures. I got a lot of hits:

The outputs provide very detail information include “secondary structure”, “chain”, “position of start and end in matched sequence”, “method of structure determination”, “source of RNA (class)”, and “resolution”.

From this search and quickly inspect the structure from the Jmol plugin, users can decide  and pick up which RNA structure fragment best fits to their purpose (e.g. linear, circular…).

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