RMSD algorithm needed

Alex Yap alexyap at betty.eng.monash.edu.au
Mon Jul 8 01:13:13 EST 1996


Hi,

Does anyone know where I can get the algorithm for 
performing minimum RMS deviation alignment between two
protein chains? 

I have a large set of protein backbone conformations expressed
as Phi & Psi angles. I have also a target (presumably native)
conformation also as a set of Phi & Psi angles. I need to
write a C-program to compare each of the conformations
in the test set against the target conformation, and calculate
the minimum RMS deviation between the alpha carbon atoms.
Since there are several thousand conformations in the
test set, I cannot use software such as Insight to perform
RMSD calculations one by one.

So, if anyone has any idea how to get such an algorithm,
please tell me where to find it.

Thanks in advance.

--
Alexander Yap
Email:
     alexyap at acslink.net.au
     alexyap at bedrock.eng.monash.edu.au
Home Page:
     http://www.peg.apc.org/~alexyap




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