Homology modelling

Andrej Sali sali at tamika.harvard.edu
Thu Oct 20 08:21:55 EST 1994


In article <37jv0i$kdm at mserv1.dl.ac.uk>  writes:
> Kaspar Hauser MD (95mhn at williams.edu) wrote:
> : Hello,
> : 	Does anyone have any experience producing a very crude
> : structural hypothesis from sequence data?  We have Sybyl, but I've
> 
> [deleted lines}
> : I've tried Sybyls built in structure-seq database, and constructed my
> : own database with many similar proteins and just the resolved protein
> : with homology.  Any suggestions or references would be appreciated,
> 
> : 				Max Nanao
> : 				95mhn at cc.williams.edu
> : 				nanao at ochre.mgh.harvard.edu
> 
> Kaspar,
> 
> Why not just directly substitute each residue [i.e. 'mutate' in Sybyl]
> in your protein of know structure for the residue in your target? If
> your target has 85% sequence similarity, this seems like a reasonable
> thing to do. Any other readers have comments about the validity of this?
> 
> Andy Sheppard
> mbasd at seqnet.dl.ac.uk

In my opinion, the resulting model is likely to be as useful for most  
problems as any other homology model. The reason is that with this high  
sequence similarity (assuming that it is sequence identity), the proteins  
are very similar.

Andrej



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