[Go] 'binding issues' item listed on the GO Consortium meetingagenda

[D'Eustachio, Peter]

... but there are ones that bind ATP and ADP but not AMP (the
transporter that exchanges ATP for ADP across the mitochondrial inner
membrane, for example).

-----Original Message-----
From: go-bounces at genome.stanford.edu
[mailto:go-bounces at genome.stanford.edu] On Behalf Of Benjamin Hitz
Sent: Monday, March 23, 2009 6:25 PM
To: go list
Subject: Re: [Go] 'binding issues' item listed on the GO Consortium
meetingagenda

>>
>
> If P binds specifically to X, and X is_a Y, then P binds  
> specifically to Y. this is built in to the is_a relation, there is  
> absolutely no getting around this.
>
> Fortunately CHEBI does not make an is_a relation directly between  
> any of these terms. Instead they are all is_a children of "adenosine  
> 5' phosphate"
>
> http://obofoundry.org/obo/CHEBI:15422+CHEBI:16761+CHEBI:16027.png
>
> (CHEBI calls this by the plural "adenosine 5' phosphate*s*", which  
> is wrong and will need to be changed in CHEBI. They are open to this)
>
> This means that if P binds to an ATP molecule, it is also the case  
> that P binds to an adenosine 5' phosphate molecule. Does this seem  
> reasonable?

That should work fine... except for those gene products which bind  
only AMP and ATP (should such a beastie exist)   I guess they can be  
annotated separately.  Or "NOT ADP binding"

>
>
>> And I suppose there are many cases where a protein can bind related  
>> chemicals with different non-zero affinities, so that if one  
>> annotated binding to one there may be a good chance it would bind  
>> another. Should there be a rule in how one interprets the  
>> annotation line so as to not read any relationships among things in  
>> the target ontology to the actual single term designated as the  
>> target for the GO annotation? (hope this is clear).fcc

This a good point and highlights another reason (perhaps not yet  
broached) that "binding" terms should be used only with extreme care -  
if at all.

What is "binding"?  Km <= 10^6?  Km < Physiological concentration  
under some condition?  The definition of GO:0005488 is hopelessly  
vague on this: "The selective, often stoichiometric, interaction of a  
molecule with one or more specific sites on another molecule."

selectivity:  undefined
"often stoichometric": often qualifier makes this irrelevent
interaction: undefined
"specific sites": undefined


Apologies in advance to GOC:ceb and GOC:mah, not meaning to critique  
your work or you personally.


Ben


--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
hitz at genome.stanford.edu



_______________________________________________
Go mailing list
Go at geneontology.org
http://fafner.stanford.edu/mailman/listinfo/go

------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================