[go] Putting method/program names into the with field for ISS (OT)

[Benjamin Hitz]

>



> Finally, your point about sequence and structure being the same.  I  
> think it is possible for two proteins to form similar structures  
> but to have quite different primary sequences.  Therefore, it would  
> be possible to have the cystal structure of two proteins, observe  
> that they are similar, and then conclude that they might share a  
> similar function.  In fact there are 4 NIH-funded centers which are  
> part of the Protein Structure Initiative which are devoted to  
> producing large scale data sets of structures, many from proteins  
> of unknown function.  So, although I have not personally done any  
> annotation of this sort, I expect that comparisons of this kind  
> will become more frequent as more structures are produced.

Yes, speaking as at least an ex-expert in protein structure, it is  
theoretically possibly to do this (make annotations based on  
structural similarity where there is convergent evolution).

I know of one case, the mouse "Tubby" protein which was correctly  
predicted (via visual inspection of the protein surface) to be a DNA  
binding protein - however, this is not via the similarity of the  
structure to any known structure (it was, IIRC, a novel fold).

I think there was also a computational technique that looked for  
protease catalytic triads in any 3D structure, but I don't think it  
works very well.

In general, however - function is inferred from homology which may be  
inferred from sequence and/or structure (in some cases).

Ben
--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu