[Molvis-list] protein visualisation

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Fri Sep 8 04:51:54 EDT 2006

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.


You need to look into 'homology modeling', which allows you to crate a 
putative structure from your sequence based on homologous proteins of 
known structures (the structures returned by blast). For an early 
example see [1]. Generally speaking the more similar your sequence to a 
protein of known structure, the more likely your protein is to have a 
similar structure [2].

As for accurately predicting the effect of mutations on the structure 
'ab-initio', that is a lot harder (I think). Its not my field, but 
perhaps people on the list can point you to work related to predicting 
the structural effect of mutations. However, you can get a lot of 
information by just looking at the region of interest on the sequence in 
the model of the structure.

1. Perutz M. 1965. Structure and Function of Haemoglobin: II. Some 
Relations between Polypeptide Chain Configuration an Amino Acid 
Sequence. J. Mol. Biol. 13:669
2. Chothia C and Lesk A. 1986. The relation between the divergence of 
sequence and structure in proteins. EMBO J. 5:823

> thanks

Your welcome!


> Phil P.
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