USF

Uppsala Software Factory - DEJAVU Package

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Manuals

Examples

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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.

Requirements

DEJAVU is available for SGI, DEC ALPHA, LINUX and OSX systems. O is handy 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


USF Latest update at 14 December, 2006.