

Dear Mr. Allen:

   There is plenty of code to do standard 1D/1D peptide sequence matching
which dates back to the Needleman-Wunsch algorithm.[1]  One package which
contains several variations of this matching algorithm is the GCG software.[2] 

[1] Needleman, S. B.; Wunsch, C. A general method applicable to the search for
    similarities in the amino acid sequence of two proteins.  J. Mol. Biol.  
    1970, 48, 444-453. 

[2] Genetics Computer Group, (1991), Program Manual for the GCG
    Package, Version 7, April 1991, 575 Science Drive, Madison, Wisconsin, 
    USA  53711.

    More recently, there has been a great deal of interest in methods for
finding which 3D protein structure is compatible with a given 1D sequence (the
inverse protein folding problem).  This software is potentially useful for
finding structures which despite their low primary sequence homology,
nevertheless share similar protein folds. Below is a summary of the responses
to my query to the bionet.biology.computational mail newsgroup
([email-masked]).

   Below is a summary of publicly or commercially available sequence/structure
matching software.  I apologize in advance for any omissions or errors. Thanks
to all that replied, especially Steve Bryant, Steve Brenner, Gordon Crippen,
Vladimir Maiorov, and David Eisenberg. 

1) Brenner ([email-masked])
   plans to make software available "once it's stable"

2) Bryant ([email-masked]), Lawrence
   The Bryant threading software is available via anonymous ftp from
   ncbi.nlm.nih.gov (130.14.25.1) in the compressed tar archive
   /pub/pkb/Threading.tar.Z. 

3) Blundell, Donnelly, Eisenmenger, Johnson, Overington, Sali, Topham,
   Blundell's Composer software is available from Tripos Associates however
   the Blundell's sequence/structure software is currently not available. 

4) Crippen ([email-masked]), Maiorov ([email-masked])
   Crippen and Maiorov's contact potential software may be obtained by writing
   Vladimir Maiorov. 

5) Eisenberg ([email-masked]), Bowie, Choe, Luthy, McLachlan, Mcleod,
   Wesson, Wilmanns, Yamashita
   Academics may obtain the 3D Structures Profile software by writing David
   Eisenberg.  Commercial sites may obtain this software through Biosymm. 

6) Jones ([email-masked]), Taylor, Thornton
   plans to make it available, but not ready yet

7) Ouounis, Sander, Scharf, Schneider
   no information

8) Sippl, Casari, Floeckner, Froschauer, Gottsbacher, Hendlich, Lackner,
   Weitckus
   no information

9) Skolnick, Godzik, Kolinski
   Sknolnick's MatchMaker software will be available from Tripos Associates.

   The following excellent reviews compare and contrast the various methods
available for sequence/structure matching. 

(1) Wodak, S. J.; Rooman, M. J. Generation and testing protein folds.  Curr.
    Opinion Struct. Biol.   1993, 3, 247-259.

(2) Fetrow, J. S.; Bryant, S. H. New programs for protein tertiary structure
    prediction.  Bio/Technology   1993, 11, 479-484.

     I hope you find the above information useful.

     Sincerely,

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| Konrad Koehler              |  Computational Chemistry Group     |
| internet:  [email-masked]  |  Department of Medicinal Chemistry |
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