How to compare 3d Protein structures?

David Jones jones at bsm.bioc.ucl.ac.uk
Wed Jun 5 12:56:30 EST 1996


Ulf Reimer (reimer at biochemtech.uni-halle.de) wrote:
: Dear Netters!

: Is there any program known which allows to compare 3D structure of
: different PDB Files?

: Thank you!

Hundreds... well, at least a hundred. SSAP by C. Orengo at UCL and
Dali by L. Holm at EMBL (EBI), are probably the best known. There is
also STAMP from G. Barton at Oxford, and many others. If you just have
some coordinates you want to scan and don't want to install any
software, then you can just e-mail the coordinates (in PDB format) to
dali at embl-heidelberg.de and wait for the search results in your mailbox.
It can also be accessed via WWW - www.embl-heidelberg.de. Otherwise you can
contact some of the above people to enquire about getting hold
of the programs concerned.

If you just want some references, then have a look at a fairly
recent review by Holm and Sander - PROTEINS (1994) Vol 19:165-173.

The actual mechanics of comparing protein structures is pretty
much a solved problem now. What really isn't a solved problem is how
to measure structural similarity after the comparison has
been completed.

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