SURFACE PREDICTIONS SUMMARY

HIDEW at SIMSC.BITNET HIDEW at SIMSC.BITNET
Wed Oct 30 09:59:00 EST 1991


SURFACE PREDICTIONS:

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I have recieved several replies on the PROTEINS board concerning
the tools out there for predicting surface residues. I have presented
here the relevant references and suggestions.:-)
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My thanks to all those who replied and made this information available.

>>>>>> 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
>
  George Rose has published a number of papers on
predicting the location of turns in the peptide chain using (I recall
distantly and perhaps incorrectly) local minima in a smoothed
hydrophobicity term.  See Nature 384:654-7 (1983) and Adv. Protein Chem
37:1-109 (1985) for more details.  This is not precisely the
question you asked but is related because the turns are usually
on the surface.

David States
National Center for Biotechnology Information / National Library of Medicine


-------------------

perhaps PROFILEGRAPH will do what you need. It runs on a PC under MSDOS and
plots various amino acid parameters over one or more given sequences. Several
meaures of surface probability are included into the program. It will not
give clear statements like: "Pos.121 through 140 are on surface" but draws
only probability curves that should be used together with the original paper
given by the authors of the parameter table. (Refs. cited in program
documentation)
The program is quite voluminous, but does a lot of other things too.
Is is available from netserv at embl-heidelberg.de by sending a mail with
an empty subject line which has in the mail-body the line:
get dos_software:prograph.uaa

I hope you can use the program,
                                 Kay Hofmann
---------------
Holbrook, S.R., Muskal, S.M., Kin, S.-H. 1990.  Predicting surface exposure of
amino acids from protein sequence.  Protein Engineering 3: 659-665.

Holbrook is from the Chemical Biodynamics Division, Lawrence Berkely Lab,
Muskal is from the Dept. of Chem, Un of California at Berkeley,
Kin is from both Biodynamics and Chem.

Dan Jacobsen

_________________
  I noticed your posting on bionet.molbio.proteins (or whatever) requesting
a program for prediction of surface residues.  It turns out that my advisor
wrote a program to predict 'flexible' residues of proteins, which turns out
to be essentially identical to predicting surface residues.  The listing of
this fairly short FORTRAN program appears in:
  Karplus,PA; and Schulz, GE (1985) Naturwissenschaften 72:212
  "Prediction of chain flexibility in proteins"

-Chris Bruns; Biochem grad, Cornell University, Ithaca, NY
YQDX at CRNLVAX5 (bitnet)
YQDX at VAX5.CIT.CORNELL.EDU (internet)
607 277 6263 (lab)



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