Welcome to the AtlasCBS server!
AtlasCBS is a tool that allows you to explore chemico-biological space using Ligand Efficiency Indices (LEIs) as variables. This unique set of variables permits a graphical representation of the content of databases that contain affinity data (SAR databases such as PDBBind, BindingDB) in an atlas-like fashion. The server allows you see the content of the database(s) of choice as pages in a map-like environment with different variables and scales. The content of the databases is displayed in two-dimensional pages where the angular coordinate is related to the chemical composition of the ligand(s) and the radial coordinate is related to affinity of the ligand(s) towards the specific target(s). Details can be found in the specific publications.
The purpose of this server is to help you navigate in Chemico-Biological Space (CBS) so that you can examine the affinity and polarity of the chemical matter available for certain target(s) and possibly compare against what your own laboratory can produce, or what your competitors are designing. This comparison can be extremely useful and can allow you to design strategies to optimize your drug-discovery projects in your academic or private research.
Currently, available databases include BindingDB, PDBBind v2010, ChEMBL 11 and private user uploaded databases. In order to use your own the private databases you have to register here
To start using the site click on Map viewer in the menu and accept the permission request for the Java Applet or use the new Map viewer here which does not require Java.
Some additional references can be found below.
- Abad-Zapatero, C.; Blasi, D.Ligand Efficiency Indices (LEI): More than a Simple Efficiency Yardstick (2011). Molecular Informatics. 30 (2-3), 122-132.
- Christmann-Franck, S.; Cravo, D.; Abad-Zapatero, C.;Time-Trajectories in Efficiency Maps as Effective Guides for Drug Discovery Efforts (2011). Molecular Informatics. 30 (2-3), 137-144.
- Blasi, D.; Arsequell, G.; Valencia, G.; Nieto, J.; Planas, A.; Pinto, M.; Centero, N. B.; Abad-Zapatero, C.; Quintana, J.;Retrospective Mapping of SAR Data for TTR Protein in Chemico-Biological Space Using Ligand Efficiency Indices as a Guide to Drug Discovery Strategies (2011). Molecular Informatics. 30 (2-3), 161-167.
We provide a set of examples to test the server. Also there is an already set up account, with several data sets, to provide a sandbox anoymous space with the following credentials:
- Username: atlas
- Password: atlas
In the following list you can download several personal data sets to be used within the server:
Guide
To analyze the different examples (to be used with the sandbox account or in a new one).Taxanes and epothilones
In this example we can compare the efficiency of taxanes versus epothilones within the human microtubule. Download: Taxanes and epothilonesVirtual Screening results analysis
In this example we can explore the results of a little screening campaign using the Directory of useful decoys sets for the Catechol-O-metyl transferase, including real drugs and very similar decoys. Download
If you encounter problems in the use of the server please consult the help section or these specific topics:
We really appreciate your suggestions, comments, ideas or whatever insight you might have. Possible ways to improve the current server and new ideas that could be useful for the scientific community at large are welcome. Please send e-mails to acortes at cbm.uam.es or caz at uic.edu. We will be delighted to hear from you.
The developers of the platform disclaim all warranties with regard to this platform, web and software, included all implied warranties of merchantability and fitness. In no event shall the developers be liable for any special, indirect of consequential damages or any damages whatsoever resulting from loss of user, data or profits, whether in an action of contract, negligence or other tortuous action, arising out of or in connection with the use or performance of this platform, software and web.