1. I have not received the email with the results link.
  2. First check the email account you used to submit calculations is valid. If it is a valid account, then check the spam inbox of your email account. Be patient, calculations can take time. If it has been more than 1 day since you submitted your calculations and you still have no results, please contact us, an error may have happened.

  3. How long will my calculations take? Can't you show me an estimation?
  4. That is difficult to foresee. Computation time depends on many factors such as the datasets to screen, the workload of the cluster or the number of results requested. Screening all the datasets proposed with one similarity method may be completed in less than 15 minutes. However, other configurations can take up to 24 hours.

  5. The JME applet for sketching molecules does not load.
  6. You may have a Java problem. Update Java to the latest release and add security exceptions for BRUSELAS site.

  7. For how long are my results available?
  8. Results remain in our server for 30 days. They will be removed afterwards and you will see the message "Not available" in the results screen.

  9. Can I share my results with anyone else?
  10. Yes, you can share your results in two different ways:
    1) Send a link by email using the "Share" icon under the query image on the results screen. Other people will receive the link to access the dashboard.
    2) Download the list of hits (names and scores) in an Excel file. Since the Excel file is downloaded on your computer, you are free to manipulate or share as you wish. This option will be available even after the 30 days period of availability of the results.

  11. What libraries can I select for screening?
  12. By default, the server provides three libraries: ChEMBL (version 21), DrugBank (approved compounds), KEGG (compounds and drugs subsets) and DIA-DB which is an ad-hoc library of anti-diabetics. You can combine them as you wish. If none is suitable for your experiment or you want to screen you own library, you have the chance to upload a custom one in one single file of up to 20MB. In that case, the filter to select the most promising ligands is not applied to preserve the library exactly as it was uploaded.

  13. What molecular formats are supported by BRUSELAS?
  14. The server relies on babel/obabel to perform format conversion, so that, any format accepted by babel/obabel is admitted (mol2, pdb, sdf, mol...). Smiles chains are admitted as well and converted to the format requested by each similarity software. BRUSELAS carries out the minimum amount of conversions because each transformation may result in a loss of accuracy. In any case, if you can choose, mol2 is the default and more suitable format.

  15. Is it possible to run docking calculations from this website?
  16. No. This server is mainly focused on ligand-based virtual screening methods. Molecular docking is a structure-based approach which is not supported by this tool yet. If you need to run docking calculations, we invite you to use Achilles.

  17. What is included in the downloadable results file?
  18. You can download the results in a .pse file which can be loaded on PyMOL as a session. The PyMOL session is organized in a hierarchy where the similarity algorithms represent the root. You can profit from this structure to display only the molecules of your interest. By default, only the five best-ranked compounds are selected, but you can select or unselect whatever compound that you wish.

  19. I have some problem or question that is not listed in this FAQ.
  20. Contact the administrator ( hperez@ucam.edu).