What is the difference between Relibase and Relibase+?
Relibase+
Relibase+ is an enhanced commercial version of Relibase. It offers all the features
of the WWW version of the program, with the added
ability to generate proprietary databases of protein-ligand complexes, and subject
them to the same searches, alongside the PDB,
confidentially on the users' own hardware. As a result Relibase+ is a powerful tool
for the investigation of binding site interactions in individual
complexes and trends through series of complexes, in publicly available data and
proprietary data. Additional features in Relibase+ include:
Protein-protein interaction searching.
Detailed analysis of superimposed binding sites.
Improved and enhanced treatment of hitlists.
Crystal packing module enabling detailed investigation of crystallographic packing effects around ligand binding sites.
WaterBase data module for deriving, storing and handling a set of descriptors for every water molecule, including an energy score and characterisation of its local environment.
Reliscript, a command-line interface to Relibase+ which allows access to PDB data and Relibase+ search methods from within the Python scripting environment.
CavBase, a program for detection of unexpected similarities amongst protein cavities (e.g. active sites) that share little or no sequence homology.
Relibase
Relibase is freely available on the WWW for academic users and features:
An intuitive web-based user interface
A fast database search engine
Standard text searching
2D substructure searching
3D protein-ligand interaction searching
Similarity searching for ligands
Automatic superposition of related binding sites to compare ligand binding modes, water positions, ligand-induced conformational changes, etc.
Clear 3D visualisation using RasMol
How can I trace problems with my Relibase+ installation?
The Help page within Relibase+ contains a troubleshooting section which can help you to identify any problems that you may be experiencing wiht Relibase+.
This includes PHP diagnostics and Apache logs (for the httpd server bundled with Relibase+).
Can I use my own HTTP server?
To establish communication between your clients and the Relibase+ server, an HTTP server is required.
You can either use the HTTP server that is distributed with Relibase+, or use your own HTTP server.
If you use your own HTTP server you need to configure it correctly, please refer to the Relibase+ Installation Guide for further information.
Is it possible to save queries within Relibase+?
Yes, queries that are set up in the sketcher can be saved by selecting the Save Query button.
Saved queries can then be read back into the drawing area by selecting the Load/Delete Query button and selecting the saved query from
those appearing in the resultant dialog box.
It is possible to export the results of a search in XML format using Relibase+ 2.0, from either a ligand or protein
results page. Clicking on the Export XML Hitlist link will allow you to define a filename and location
for the hitlist XML file.
Is it possible to share hitlist data with other Relibase+ users?
The simplest way to do this is to export a hitlist as XML (see above) and then use the "Read XML format Hitlist" option from within the Hitlists section
of Relibase+.
Sharing of hitlists can also be accomplished with reliscript. Ensure you are logged on as the user who owns the hitlist to be shared, check that the standard Relibase+
environment is set up and start Reliscript with the commands:
(e.g. "setenv RELIBASE_DATABASE reli" if the hitlist was created using the standard reli database).
python
You should now see the Reliscript >>> prompt. From here type:
import reliscript as rs h = rs.set('ligand','hitlist_name')
where "hitlist_name" is the name of the hitlist you want to transfer. For example, if the hitlist was saved as
"SAVE1" you would type h = rs.set('ligand','save1')
rs.use_workspace('new_user')
where "new_user" is the name of the user's workspace you want to copy the hitlist to (e.g. to save to user1's
workspace, type rs.use_workspace('user1')
h.save_to_hitlist('hitlist_name')
This should then save the hitlist to the new user's account.
Is it possible to share superposition data with other Relibase+ users?
Yes. Superposition data is stored in $RELIBASE_ROOT/DATA/SUPERPOS in folders with the
naming format username_savename. So if for example you saved superposition
data as superposition whilst logged on as user2, this would be saved in the directory user2_superposition.
To allow
other users to access this, copy the directory and all of its contents and rename the first part
of the folder to the name of other user who you wish to share the data with, i.e. to allow user user3 to access the the data
from the above example, rename the folder to user3_superposition.
Can I search for structures that satisfy a logical combination of text queries. For example, compounds which have method set to X-RAY but not to NMR?
Yes, set up a keyword search on 'X-ray' and save the hitlist before running the search by entering a name in the
Save in hitlist box. Conduct a second search on 'NMR' and again save the hitlist. Click on "Hitlists" and go to "protein set 1" and select the X-ray hitlist, then for "protein set 2" select the NMR hitlist. Change the hitlist operation to "not", this then
gives a hitlist consisting of proteins containing the word X-ray and not NMR.
