[Molvis-list] protein visualisation

[Annemarie Honegger]

Dear Phil

Even for experts it can be years of hard work to convert a Fasta
Sequence into a 3D structure, as it usually involves first producing
enough of the protein (some, especially membrane proteins, can
still be very hard to produce in sufficient amount in native form),
then growing crystals (often trying hundreds of conditions, but
some protein still will not produce crystals of sufficient quality),
then measuring the pattern produced by diffracting X-rays on
  these crystals, and eventually trying to make sense of these pattern.

However, somebody else may already have investigated your protein
in this manner. Therefore take your protein sequence to the
protein database (http://www.rcsb.org) and, under "advanced search",
choose a blast or fasta-search with your sequence.If your lucky, you  
find ¨
at least a closely related molecule amongst the 38'620 Structures
currently in the database. If your sequence is very long, your
protein structure may be composed of more than one domain (independent
folding unit), and you may find different structures matching
different part of your sequence.

If you find a close match, but would like to have a model with your  
exact sequence,
you may try the swiss-model repository of homology models http:// 
swissmodel.expasy.org/
or the modeling server http://swissmodel.expasy.org/.  However,
be aware that these are just automatically generated models with
all the limitations inherent in the process! What this server  
basically does
is to apply the backbone conformation of the most closely related
proteins to your sequence, and change the side chain coordinates
to reflect your own sequence, using both the conformations of the
amino acid originally present and the rotamer preferences of the
different amino acids into account. As a result, you get multiple models
reflecting the different template structures available amongst the  
known structures.

The model will not predict structural or conformational changes
due to point mutations, although it will help you to identify
potentially destabilizing substitutions, especially if they result in  
steric clashes.

                           Annemarie





On Sep 8, 2006, at 4:26 AM, Phil Princely wrote:

> hi all
>
> I'm new to this list, and a complete newbie when it comes to protein
> visualisation, so I hope this question is ok.
>
> I'm looking for a way to convert a fasta sequence of amino acids  
> into a
> picture of a protein. I've used various sites on thei web, but all  
> of them
> used a blast like search to tell my proteins which were similar to  
> my fasta
> sequence, and gave me their structure.
>
> I don't mind if the representation isn't accurate, because I'm more
> interested in whether a change in part of the sequence will have an  
> effect
> on the final shape. So I don't need great accuracy, just a rough  
> shape.
>
> I'm pretty sure that this ab-initio kind of protein visualisation  
> isn't yet
> possible with just one computer, but maybe somebody could point me  
> in the
> right direction.
>
> thanks
>
> Phil P.
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