Surface Prediction

usercu11 at mts.ucs.ualberta.ca usercu11 at mts.ucs.ualberta.ca
Tue Oct 29 11:09:27 EST 1991


In article <BASHFORD.91Oct23113347 at zerbina.scripps.edu> bashford at scripps.edu
(Don &) writes:
>>>>>> On 19 Oct 91 19:24:00 GMT, HIDEW at SIMSC.BITNET said:
>
>HIDEW> I am seeking a surface prediction program that will run on VMS or PC or
MAC.
>
>HIDEW> preferably the latter. I am aiming to correlate surface predictions
with
>HIDEW> conservation across taxa.
>
>HIDEW> Any one know of a workable program that will do surface predictions?
>HIDEW> (from aa seuqnce of course).
>
>I'm not sure what you mean by "surface predictions", but you may be
>interested in a paper by myself, Cyrus Chothia and Arthur Lesk,
>J. Mol. Biol. vol. 196, pp 199-216 (1987).  It describes a sequence
>template characterizing the globin family which includes some
>unexpected conservation rules at surface sites.
>
>I can make the computer program and templates available to you.
>They are written in C and, in older versions, ran on a VAX, but
>now run on Unix.  They could probably be re-ported to the VAX without
>too much trouble, although I understand the VAX C compiler is buggy.
>
Synthetic Peptides Inc. (c/o Dept. of Biochemistry, Univ. of Alberta, Edmonton,
Canada T6G 2H7) sells a PC program called SurfacePlot that predicts surface
residues. It is intended to identify stretches of sequence that could be useful
as synthetic antigens.

>
>HIDEW> Win Hide
>HIDEW> Laborator of molecular systematics
>HIDEW> Smithsonian Istitution
>HIDEW> Washington D.C.
>HIDEW> 301 238 3444
>HIDEW> hidew at simsc (bitnet)
>
>Donald Bashford
>Department of Molecular Biology
>The Scripps Research Institute
>10666 North Torrey Pines Road
>La Jolla, CA  92037
>USA
>



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