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. If you sent me a reply and it
bounced back to you, please try sending it again since we have been having
problems with our internet connection. It seems to be working now.
1) Brenner (seb1005 at mbfs.bio.cam.ac.uk)
plans to make software available "once it's stable"
2) Bryant (bryant at melanie.nlm.nih.gov), 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 (crip at phar.umich.edu), Maiorov (wowa at phar.umich.edu)
Crippen and Maiorov's contact potential software may be obtained by writing
Vladimir Maiorov.
5) Eisenberg (david at uclaue.mbi.ucla.edu), 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 (jones at bsm.bioc.ucl.ac.uk), 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.
