Uppsala Software Factory

Uppsala Software Factory - SPASM Package

Manuals

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)

Related freebies

Trouble ftp-ing through your browser ? Look here !
Dennis Madsen has written a SPASM server. If you are in Uppsala, you can use the full-blown version on the intranet server. Otherwise, you can use this public version. If you want to install a SPASM server locally, contact Dennis for a copy of the Perl script.
uniquefy_objects.csh, script to uniquefy object names in a SPASM or SAVANT O macro
ftp_hits, 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

Description

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 poor hits
SAVANT - to do all-atom superpositioning of SPASM hits

Requirements

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 Data Bank.

References

GJ Kleywegt, JY Zou, M Kjeldgaard & TA Jones. International Tables for Crystallography, Volume F. Chapter 17.1, pp. 353-356, 366-367 (2001).
GJ Kleywegt, J. Mol. Biol., 285, 1887-1897 (1999).
GJ Kleywegt & TA Jones, Acta Cryst., D54, 1119-1131 (1998).

Latest update at 20 September, 2002.