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protein / predicting 3D-structure perturbation

Marketa J Zvelebil marketa at ludwig.ucl.ac.uk
Fri Sep 12 16:43:11 EST 1997


Scott Le Grand wrote:
> 
> Michel PETITJEAN wrote:
> >
> > I have the x,y,z coordinates of a protein in PDB format.
> > One of the residues has an H-bonding with the rest of the protein.
> > Now I replace this residue with an other one which offers no H-bonding.
> > How can I predict the perturbations induced on the 3D-structure ?
> > Is there softwares for that (free or not) ?
> > Thanks.
> 
> There are numerous prediction packages available.  None of them
> have been shown to be of any predictive value whatsoever anywhere
> but within the scientific papers that describe them.  However,
> I'm sure the developers of said packages would insist on
> disagreeing with this statement
> 
> Your best bet at prediction would be to assume the structure
> did not change as a result of the mutation.
> 
> Scott Le Grand

It would depend what kind and how large are the perturbations you
want to measure. Easiest is to model the mutation as you have and
simply minimize the structure and look at local changes. If you want
to go further you can try local dynamics. If you really want to get
deeply into it, with probably very little extra information, you
could try things like how has it effected the charge distribution
around that residue etc. That is all available within insightII
(Biosym).

Marketa


-- 

                  Dr. Marketa J Zvelebil,
Ludwig Institute for Cancer Research, 91 Riding House Street			
                  London W1P 8BT, ENGLAND.				 
       Tel: (44) 0171 878-4012 ,Fax: (44) 0171 878-4040			
              e-mail: marketa at ludwig.ucl.ac.uk	  
          http://www.ludwig.ucl.ac.uk/st/hello.html 
                              *
        "Computers make excellent and efficient servants 
           but I have no wish to serve under them."
               (Spock - The Ultimate Computer)





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