[Molvis-list] Re: protein visualisation

[Phil Princely]

hi all

thank you to everyone for taking the time to answer my question.
through all of your anwers, i've learned a lot about visualisation.

the protein that i am looking at only had a 30% similarity with known
proteins, and the results that i got when i looked it up were just the
shape of the most similar protein. when i saw the .pdb file, i
originally thought that the website had produced it for me, but then i
figured out that it was the shape of a protein already determined by
x-ray crystallography.

i was also advised to compare the mutant section in blast servers to
see if there are any other proteins it might be in. the reason is to
investigate why one organism is benign, while a similar one (with the
mutations) is not.

thanks again for all your suggestions.

Phil P.

On 9/8/06, Diana Irwin <di12 at cornell.edu> wrote:
> Dear Phil,
> You can send your amino acid sequence (do not include the period at
> the end) to swiss model.
> http://swissmodel.expasy.org//SWISS-MODEL.html
> It will use a blast program to match your protein to proteins with
> known structures.  You will receive a file via email containing your
> sequence and any matches swiss model can find.  This file can then be
> opened from within Swiss PDB Viewer and you will see all of the files
> of all the relavent sturctures in the control panel window.  If you
> are new to Swiss PDB Viewer it is important and well worth the time
> to work the tutorials from Gale Rhodes. This very sophisticated and
> useful program works well with PCs and Macs and it is FREE!
>
> Diana Irwin
>
>
> >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.
> >_______________________________________________
> >Molvis-list mailing list
> >Molvis-list at bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/molvis-list
>
> _______________________________________________
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/molvis-list
>