Uppsala Software Factory - SPASM Package
Download executables (SGI|ALPHA|LINUX|OSX) |
Download databases & libraries |
- SPASM to find motifs of main and/or
side chains (includes MKSPAZ documentation)
- SAVANT to do an all-atom
superpositioning of SPASM hits
(Example: top four hits
for the Met-Trp interaction in the interface between
acetylcholinesterase and fasciculin II, after prrocessing with
SAVANT using only the side-chain atoms)
- RIGOR to find predefined motifs
from other structures in your model (includes MAKRIG documentation)
- DEJANA to sort hits in an O macro generated by SPASM (documentation
can be found in the DEJAVU manual)
- Trouble ftp-ing through your browser ?
Look here !
- Dennis Madsen has written
a SPASM server. You can use this
public version. If you want to install a SPASM server locally,
for a copy of the Perl script.
script to uniquefy object names in a SPASM or SAVANT O macro
script to ftp the PDB files of "hits" found by SPASM if these
are not available locally
- Tutorial: Recognising
a motif from your protein in other protein structures, using
SPASM, SAVANT, DEJANA, and O
SPASM is a suite of programs related to DEJAVU. Whereas
DEJAVU can be used to try and recognise entire domains or molecules
(fold recognition), SPASM works at the level of smaller motifs
of main chain and/or side chain arrangements. For example, if you solve
a new structure you may want to know if there are other proteins which
have a similar set of catalytic or substrate-binding residues.
Alternatively, you may encounter an unusual loop and want to check if
it occurs in other proteins.
The package consists of of the following programs:
- SPASM - this program takes a user-defined motif of main chain and or
side chains and compares it against a large database derived from the PDB. All
hits are listed in the output. In addition, an O macro is generated
that, when executed inside O, will read, superimpose and display all
proteins that were matched in the database (this requires that you have a local
copy of the PDB database). Also, an input file can be generated for the
least-squares superpositioning program LSQMAN (part of the DEJAVU
package), which will help you to determine if any similarities with structures
found in the database extend beyond the motif.
- MKSPAZ - the PDB-derived database that SPASM uses contains
coordinates only for the CA-atoms and the centre-of-gravity of each residue's
side chain atoms. MKSPAZ is a little utility program with which you can
generate your own SPASM database, e.g. of in-house structures
which are not (yet) in the PDB.
- RIGOR - this program does more or less the opposite of SPASM.
It searches a database of pre-defined motifs to see if any of them occur in
your own protein structure. An O macro can be produced that will display the
parent structures of any matches properly oriented on top of your own model
(this requires that you have a local copy of the PDB database).
- MAKRIG - this utility program can be used to generate your own motifs
for inclusion in the RIGOR database.
- DEJANA - to sort SPASM, SAVANT and RIGOR hits and to remove
- SAVANT - to do all-atom superpositioning of SPASM hits
SPASM is available for SGI, DEC ALPHA, LINUX and OSX systems.
O is handy for visual inspection of the "hits", which can only
be carried for those protein structures in the PDB which you have
available on disk locally, which may require a license from the Protein
- GJ Kleywegt, JY Zou, M Kjeldgaard & TA Jones. International
Tables for Crystallography, Volume F. Chapter 17.1, pp. 353-356,
- GJ Kleywegt, J. Mol. Biol., 285,
- GJ Kleywegt & TA Jones, Acta Cryst., D54,
Latest update at 1 July, 2004.