[3dem] ColoRNA -- software to map 3D RNA changes onto secondary structure

Joachim Frank jf2192 at columbia.edu
Tue Feb 26 07:22:54 PST 2013


ColoRNA is software written 7 years ago in my lab by Jamie LeBarron.  It 
was recently revived by an update of interfacing tools and addition of a 
tutorial in Ning Gao's lab by his student Ningning, at Tsinghua 
University, Beijing.

Its purpose is the following: if you have two versions of an RNA 
structure (given as pdb files), differing as a consequence of 
conformational changes, and given the secondary structure, then the 
program is able to determine the distances between corresponding 
residues and heat-map them onto the secondary structure.  That is, very 
mobile/flexible residues show up in red, moderate ones in yellow and 
green, very stable ones in blue.

So it is possible, with the aid of this program, to determine which 
parts of the secondary structure are responsible for the mobility of the 
3D structure.

LeBarron, J., Mitra, K., and Frank, J. (2007). Displaying 3D data on RNA 
secondary structures: coloRNA 
<http://www.sciencedirect.com/science/article/pii/S1047847706002814>. J 
Struct Biol 157, 262-270. PMID: 17070699

You can find the software and documentation by following this link:

http://franklab.cpmc.columbia.edu/franklab/research/software  and look 
for "ColoRNA".

--Joachim.

-- 
Joachim Frank, Ph.D.
Howard Hughes Medical Institute Investigator,
Professor, Department of Biochemistry and Molecular Biophysics,
and Department of Biology, Columbia University,
650 W. 168th Street, P&S Black Building 2-221
New York, NY10032
(T) 212 305-9510
(F) 212 305-9500
(E) jf2192 at columbia.edu
http://franklab.cpmc.columbia.edu
http://www.hhmi.org/research/investigators/frank.html

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