Root mean square distance between two known structures?

Randal R. Ketchem rrk at iris3.chem.fsu.edu
Tue Mar 16 21:45:30 EST 1993

In article <113595 at netnews.upenn.edu> duong at chestnut.chem.upenn.edu (Duc Duong) writes:
>does any one know a software (PD or commercial) that will compare 3D
>structures of two proteins by measuring minimum possible root mean
>square bwetween equivalent C alpha positions? 

You could write the code yourself with the following information:

First the two structures must be superimposed. See:
Kearley, S.K., J. Comput. Chem., 11, 1187-1192 (1990).
Next you can calculate the distances between atoms (in C) with:
d = sqrt(pow(atom1[X] - atom2[X], 2)
       + pow(atom1[Y] - atom2[Y], 2)
       + pow(atom1[Z] - atom2[Z], 2));
Square all of the distances, average the squares, and take the square root.
That's all!

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