Main page

About GASS

GASS-WEB is a user-friendly web server for active site search based on genetic algorithms. It can be used under two different scenarios:

• CSA Site Search (1): Given a protein of interest, try to match a set of specific templates (i.e., known active sites) annotated at the Catalytic Site Atlas (CSA).


• NCBI Template Search (2): Given an active site template provided by the user, look for it in a database of protein structures derived from the NCBI-VAST data set.

Submission page

How to run GASS-WEB

To perform a site search based on the list of templates from the Catalytic Site Atlas:

• Click on "CSA Site Search" (1) to open the submission page.


• Provide the protein structure by either uploading your own file (2), which must comply with the PDB format, or supplying a 4-letter PDB code.


• The next step is to choose the template size for matching (3), which is the number of residues of the active site.


• You are then readu to submit your query to GASS-WEB (4).

Results page

Results

For a CSA Site Search query, your results will be displayed in a table format with the following information:

• Job ID - which can be used by the user to retrieve the results later (1), by adding it to the web server URL following the format: http://gassweb.dcc.ufmg.br/prediction/job_id

• Fitness score of matched residues - modified RMSD (2).

• List of residues found by GASS-WEB on input structure matching a template (3).

• PDB ID of matched template (4).

• Residue list of matched template (5).

• EC Number (6), Uniprot accession code (7) and resolution (8) of matched template.

The results may also be downloaded as a tab-deparated file (9).

Contact page

Getting in touch

In case you experience any trouble using GASS-WEB or have any suggestions or comments, please do not hesitate in contacting us (1) either via e-mail or through the online form.