[Molvis-list] protein visualisation

John Ferguson ferguson at bard.edu
Fri Sep 8 09:00:21 EDT 2006


If (and only if) your sequence has substantial similarity to that of a 
previously described protein whose three-dimensional structure has been 
determined by X-ray crystallography or NMR, you can use MODELLER 
<http://salilab.org/modeller/> to make a three-dimensional model of your 
sequence as a .pdb file which you can visualize with many of the pieces of 
software mentioned regularly in this forum.

We have used MODELLER successfully in our lab, but the initial learning 
curve is pretty steep.  Comprehensive documentation is provided, however, 
and I recommend it.


John B. Ferguson
Biology Program
Bard College
Post Office Box 5000
Annandale-on-Hudson NY 12504-5000 USA

INTERNET:  ferguson at bard.edu
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Professor, Biology
Health Professions Advisor

Quoting Phil Princely <phil.princely at gmail.com>:

> 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 
> right direction.
> thanks
> Phil P.
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