Two free new web servers in Uppsala for structural bioinformatics

Gerard "CD" Kleywegt gerard at xray.bmc.uu.se
Mon Dec 18 14:37:26 EST 2000



   SPASM and DEJAVU - Recognise your protein's structure !
   =======================================================


Two new web servers are available from the Uppsala Software
Factory. They are run on a dedicated server for the outside
world and may be used by anyone, free of charge. Both only
require a web browser (e.g., Netscape) and a graphical
molecule viewer such as Rasmol, Chime or SwissPDBviewer.


The first server, SPASM, is used for the recognition of small
spatial motifs (e.g., a set of active-site or ligand-binding
residues, or a "strange" loop, etc.) in a large database of
protein structures.  The user is guided from uploading a small
PDB file containing the motif of interest via specification of
the search criteria (with sensible default values) to displaying
the hits in your favorite graphical molecule viewer program.
The server is available from:

        http://portray.bmc.uu.se/spasm


The second server, DEJAVU, is used for fold recognition. The
user is guided from uploading a PDB file containing the
structure/domain of interest via specification of the search
criteria (again with sensible default values) to displaying
the hits in your favorite graphical molecule viewer program.
The server is available from:

        http://portray.bmc.uu.se/dejavu


References:
Servers: Madsen, D. and Kleywegt, G.J. (2001). To be submitted.
SPASM:   Kleywegt, G.J. (1999). Recognition of spatial motifs
         in protein structures. J Mol Biol 285, 1887-1897.
DEJAVU:  Kleywegt, G.J. and Jones, T.A. (1997). Detecting
         folding motifs and similarities in protein structures.
         Meth Enzymol 277, 525-545.


--Dennis Madsen (dennis at xray.bmc.uu.se)

--Gerard Kleywegt (gerard at xray.bmc.uu.se)



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