AW: AW: [-empyre-] recapitulating...

["NAME" <blank@el36.de>]

Are you basically coding each of the amino acids as a specific letter 
> in the alphabet? If so, how did you choose the coding or is there a
> standard scheme generally accepted in chemistry?

hello,
there is a standard nomenclature for aminoacids in one or three letters
code (for example: a= ala that represents alanine)

One interesting point
> is that although connected in chains, are proteins 3 dimensional, such
> that many of their properties are derived from their 3D shape and the 
> self-connections of the chain?

a protein can have four stages of structure
1. primary structure:
the sequence that codifies the aminoacid composition of the protein

2. secondary structure:
structural motives that result from specific parts of the sequence

3. tertiary structure:
the complete 3d structure of a protein that is related to its sequence
and composed from the structural motives.

4. quaternary structure:
some proteins are composed of more than one unit (more than one tertiary
structure)


If we were to reverse the metaphor,
> perhaps we could create a human language that was 3D, such that
> meaning could be derived along multiple paths of script instead of 
> just linearly. Almost like speaking in crossword puzzles.

generally even this would be possible. the problem is, that for this a
3d dicionnary of words (like the japanese/chinese symbols that represent
something)
had to be created.
at the moment we (the scientists+me who are working on the
www.peptomics.org project) are beginning to create the words that
depending of 
the protein can have different 3d strucure.
aditionally we are developping a font, which can be used to type a text
on the computer. the thing is, that in this case, the symbols, which
represent the words do not have an existing protein as their equivalent.




>
> I'd like to hear more about your project and what ideas you're
> exploring. Seems like there are some overlaps in my GCS system, 
> although the implementation and method sounds wildly different.


what is your GCS system ?
which methods do you use ?
do you collaborate with scientists ? where ?
why ? how ? when ? how much ?
i am working here on the project with a structural biologist in munich.
maybe we can setup sth. together. in munich or online or somewhere you
live. we have an exhibition room here...

greetings + good 2006 .

johannes blank