Request for information

S. Billakanti srb at chimera.lanl.gov
Wed Jun 14 22:41:14 EST 1995


We are in the process of creating an immunological database and epitope
maps of HIV-1 proteins.  When the epitopes are linear, such maps are
straight forward. Some of the antibody epitopes are non-linear, however,
and are conformation dependent.  Mutational analysis can pick out
positions very distant in terms of the primary protein sequence that can alter
the binding of some of these conformational antibodies.

We were wondering if anyone had software available that treated a protein
like a string of beads, labeled with the amino acid one letter
code, that allowed one to drag and move and manipulate the string
at will. Most of the very pretty pictures I have seen of this sort
in HIV work I think were created by hand, with the artist adding and
placing each "bead" one at a time. It would be optimal if we could
create a picture that 1) kept track of the protein sequence, 2)
kept track of the Cys-to-Cys bridges and 3)
that could be modified to bring into close proximity regions that are
known to influence antibodies that bind to non-contiguous sites.

There is no crystal structure for most of proteins we are going
to be dealing with.

Thanks in advance.

--srb





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