Generating molecular replacement models

sucha at sucha at
Thu Dec 16 13:31:55 EST 1993

In article <2eonu8$skr at>, rfaber at ( Rick Faber) writes:
> We're looking for a quick way to make molecular replacement models. 
> The ideal program would use a file containing sequence of the 
> unknown structure to pare down a coordinate file of a known
> structure  (assuming the sequences are already aligned).  
> Ideally the resulting output file would contain only atoms common to both
> structures.  
> ie
> sequence of	sequence of 
> unknown 	known               search
> structure       structure           model
> --------        ---------           _______
> Phe		Tyr         --->    phe
> Ser             Thr         --->    ser
> Gly 		*           --->    gly
> Cheers,
> Rick


We have developed a homology modeling program called FOLDER, which, among other
things, uses a sequence alignment and a template to identify topologically
equivalent atoms between the model and the template. It writes a PDB file for
those atoms of the model that can be assigned coordinates using the template 
and the given sequence alignment. It seems like this module of FOLDER is 
precisely what you are looking for. This work is published in Protein Science 
(Srinivasan et al. 2, 277-289) and a popular article appears in December 
issue of Bio/technology.

Hope this helps.

Sucha Sudarsanam
sucha at

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