Dear,
The antibodies recognize non-continuous epitopes that means
conformations or #-D structures. So it is difficult to predict the 3-D
structure and hence the residues which might induce antibodies.
However, researchers have tried to predict the antigenic sites in
primary protein structures. They used the physicchemical propreties
and some modified scales. If you need I can give you a cople (around
10-15) software and web servers which utilize the antigenicity scales
and can predict antigenic sites.
I give you a practical example. One of the scientist (a hard core
molecular biologist) in our institute was working on a protein in
yeast. He was unable to putify that. As a student I went to him and he
put the same problem. We predicted the possible antigenic regions and
synthesied peptides. Now we are trying to purify the protein by
affinity chromatography with antibodies.
I hope I am clear with my words and you get some thing from this
non-sense.
Harpreet Singh
"k" <knucleus at hotmail.com> wrote in message news:<iAFA7.100702$oa2.32644086 at news2.rdc1.ab.home.com>...
> Harpreet,
>> Has similar work been done with Antibodies?? I'm not an immunologist by
> trade (I'm a molecular biologist) but I do like to reading about immunology
> and it would seem to me that if you can predict peptide binding for MHC why
> not antibodies?
>> thanks
>> Brad Thomas
> Alberta Cancer Board
> Biochemistry and Molecular Biology
> Calgary AB
> Canada
>>> "Harpreet Singh" <hsingh at imtech.res.in> wrote in message
> news:46fa3a38.0110040021.10b3ed4b at posting.google.com...> > Dear
> > I am sorry that I did not provided the www location of server. It can
> > be accessed at http://www.imtech.res.in/raghava/propred . The server
> > is accepted for publication in Bioinformatics as application note.
> >
> > Again suggestions/comments are wellcome
> > Harpreet Singh
> >
> > "Michael J. Palmowski" <alphahelix at hotmail.com> wrote in message
> news:<cPyu7.24370$qi.3277053 at news2-win.server.ntlworld.com>...
> > > Dear Harpreet,
> > >
> > > thanks for posting the news. Is the website already active? what is the
> > > address (URL)
> > > of the server?
> > >
> > > regards
> > >
> > > Michael
> > >
> > > "Harpreet Singh" <hsingh at imtech.res.in> wrote in message
> > > news:46fa3a38.0110022146.632ab22b at posting.google.com...> > > > Dear
> > > >
> > > > I need your suggestion. I have developed the webserver employing 51
> > > > HLA-DR matrices from literature by Struniolo et al., 1999. The server
> > > > can deliver online predictions in graphical or HTML formats. It may be
> > > > useful in selecting promiscuous or allele specific MHC class II
> > > > binders.
> > > > What I ask from you is the additional features which you think would
> > > > improve the applicability of server
> > > >
> > > > Thanks
> > > >
> > > > Harpreet Singh
> > > > Research Fellow
> > > > Bioinformatics Centre
> > > > Institute of Microbial Technology
> > > > Chandigarh, INDIA.
