Uppsala Software Factory - DEJAVU
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Manuals
- DEJAVU to find motifs and to
recognise other proteins with a similar fold (includes
documentation for DEJANA, PRO1, PRO2 and POST)
- LSQMAN to superimpose and analyse
multiple models and/or molecules
Description
DEJAVU is a program that will help you find out if the fold of
(a part of) your protein occurs in any other protein in the
Protein Data Bank (PDB). The program compares the spatial orientation
of (a subset of) the secondary-structure elements (SSEs) in your protein
with that of a database of SSEs which is derived from the PDB (and
updated once or twice a year).
DEJAVU can produce a macro for O which will show your
protein with each of the hits found in the database superimposed on
top of it. Alternatively, an input file can be generated for the
least-squares superpositioning program LSQMAN (included in this
package). This program can perform rapid improvement of the
least-squares operator of the hits. The results of both DEJAVU
and LSQMAN can be "filtered" by another utility program,
DEJANA. This can be used to remove spurious matches.
DEJAVU also supports the use of SSE files derived from a skeleton
("bones") to compare these against the database, even though the
connectivity and directionality of the SSEs may be unknown. Bones-based
SSE files can be generated manually, or using programs from the
RAVE package (ESSENS, SOLEX).
The least-squares superpositioning program LSQMAN is also a
powerful tool for analysing multiple models or molecules (e.g.,
in the case of NCS-related molecules and NMR ensembles), and it can be
used for "biomolecular morphing" to visualise conformational differences
between two forms of a protein.
DEJAVU comes bundled with SSE databases, various pre- and
post-processing programs and a C-shell script for generating SSE files
from PDB files.
Platforms
DEJAVU is available for SGI and DEC ALPHA/OSF1 workstations.
O is required for delineating SSEs and for displaying "hits".
The latter can only be carried for those protein structures in the
PDB which you have available on disk locally (at the very least,
all CA-coordinates), which may require a license from the
Protein Data Bank.
References
- GJ Kleywegt & TA Jones, Meth. Enzymol.,
277, 525-545 (1997).
- GJ Kleywegt & TA Jones, Acta Cryst., D52,
842-857 (1996).
- GJ Kleywegt & TA Jones, Structure, 3,
535-540 (1995).
- GJ Kleywegt & TA Jones, CCP4 Proceedings,
1994, 59-66.
Latest update at 6 February, 1999.