HELP!!! Protein Graphics!!

Orhan Ertughrul owde100 at bioc.cam.ac.uk
Wed Jan 25 06:02:23 EST 1995


In article <3g4ku9$83s at news.iastate.edu>, pedro at iastate.edu (Pedro M Coutinho) writes:
 > 
 > Hi!
 > 
 > In article <1995Jan24.173624.8430 at alw.nih.gov>, johnk at spasm.niddk.nih.gov (John Kuszewski) writes:
 > |> In article <3g18fo$no3 at bigblue.oit.unc.edu>, fisher at radonc.unc.edu (Robert Fisher) writes:
 > |> |> HELP!!!!  I need to find a program that will generate PDB code if
 > |> |> given a protein sequence. 
 > |> 
 > |> Aren't we all, brother, aren't we all.
 > 
 > If you protein is homologous to one of the proteins present in the PDB
 > why don't you try the Swiss-Model Server ? The URL is
 > 
 > http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html
 > 
 > Take time to analyze the results but if you just need a quick
 > structure of your protein this works fine!
 > 
 > You get your model back in less than 30 minutes by email !...
 > 
 
Remember though that it is only a model! Sometimes it's possible
to miss things even in crystal structures because the crystal 
latice may cause a protein to adopt a position that hides features.
Recently molecular dynamic work on a protein (I forget which one) 
revealed a channel to the active site that wasn't obvious from
the crystal structure for the previous reason. 

If we can miss things in a crystal structure because we don't take
into account the experimental aspects of the procedure used to
create the structure, how much more careful is it necessary to
be when attempting to interpret what is, after all, little more
than educated guess work? Models can provide an important insight
into the structure of a protein, more so if the homolgy of homologues
used to create them is high, however, they should never be accepted
as an accurate representation of a protein's structure. For this we are
sadly still reliant on the skill of crystallographers and NMR specialists.
*8)

Orhan.

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