RE: protein entities (was Re: Rules (was Re: Ambiguous names. was: Re: URL +1, LSID -1)

---- Original message ----
>Date: Thu, 19 Jul 2007 16:29:18 -0400
>From: Michel_Dumontier <Michel_Dumontier@carleton.ca>  
>Subject: RE: protein entities (was Re: Rules (was Re: Ambiguous names. was: Re:  URL +1, LSID -1)  
>To: Darren Natale <dan5@georgetown.edu>, Michel_Dumontier <Michel_Dumontier@carleton.ca>
>Cc: Eric Jain <Eric.Jain@isb-sib.ch>, Alan Ruttenberg <alanruttenberg@gmail.com>, Chris Mungall <cjm@fruitfly.org>, Bijan Parsia <bparsia@cs.man.ac.uk>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
>
>
>Darren,
>
>> Also, while we recognize
>> that there are different qualities that can be ascribed to a basically
>> identical biochemical entity in different structural conformations or
>> states of ligand binding, we are not attempting (at least in the
>> beginning) to describe these structural conformations or bound vs
>> unbound forms.
>
>Indeed, while conformation is an important quality of molecular
>structure, it does not fundamentally change the nature of the molecule.
>i.e. a protein in a bound or unbound state should still be considered
>the same protein. 
>
>Cheers,
>
>-=Michel=-
> 
>
Many post-translational modifications like glycosylation (http://www.functionalglycomics.org/static/index.shtml)in proteins fundamentally change the (functional) 'nature' of the protein (as also the molecular structure of the protein in case of glycosylation through addition of sugar chains (glycans)).

Satya Sahoo

Knoesis Center
http://knoesis.wright.edu

Received on Thursday, 19 July 2007 20:59:07 UTC