Welcome to DASP!
The DASP PDB and GenBankNR database was last updated October 2011.
Older DASP versions still available: November 2010 ; January 2009 ; January 2008 .
Enter your query information following the directions below. See the User's Manual for more details.
PDB and GenBankNR databases last updated in October 2011.
Enter User Information
Creating an Active Site Profile
- E-Mail Address: Enter a valid email address that the results can be sent to. Make sure it is correct or you will not receive your results.
- Job ID: Enter a name for your query so that you may easily identify the emailed results. Do not include spaces in the job name.
Performing a Database Search
- Protein PDB name and key residue information: You may enter in as many PDBs as you like, but each must have at least one key residue identified.
This field requires a specific format.
To specify a PDB entry, enter 'PDB' then the 4 character pdb id followed by the chain. If only one chain is present then enter 'A' for the chain. Using 1AAZ as an example this looks like: PDB1AAZA
Next enter the key residue information. The PDB entry is followed by a colon ':', then ONE space, then each of the key residue numbers. Key residue numbers are separated by a comma and NO SPACES.
For example PDB1AAZA: 1,2,3
If you have a list of PDB entries and key residues already in the right format, you may copy and paste them into this field. Also, PDB entries may be specified using upper or lower case, and you must enter one or more key residues for each PDB entry.
- Profile Radius: The profile radius specifies the size of the inclusion sphere around the center of mass for each key residue. Any residue inside the inclusion sphere of at least one key residue will be included in the ASP. The default is 10 angstroms, but you may increase or decrease this number as you see fit.
- To create the ASP from the information entered in the previous steps, press the 'Create ASP' button. Progress will be displayed in the status window at the bottom of the form. If there are any errors, or one of the PDB entries you specified could not be found a message will appear in the status window. In order to create an ASP all PDB entries must be valid, so if one cannot be found it must be removed before an ASP can be generated.
The status window will display the name of the key residues for each pdb entered; this is the time to ensure that you have entered in the correct number for your residues.
- Once the ASP is successfully created it will appear in the Creation Window and results will be emailed to you. In the Creation Window you may copy and edit the ASP as necessary.
These edits will be implemented in the sequence database searching, should you wish to go on to conduct these searches.
- Once an ASP has been created you can search either the PDB or GenBankNR databases for significant matches. Note that this applet is being executed on your computer so your browser must stay open and active while the search is in progress or it will be terminated. Both of these searches take a long time to complete (up to 24 hours) dependent on what hardware you are using, so be sure you are able to leave your computer on for the duration.
- P-value significance cutoff: Enter a number to use as the p-value cutoff. A higher number equals a higher significance level (lower p-value). Only results at this significance level or greater will be returned. Generally a number between 5 and 10 works well.
- Search database: Specify the database you would like to search. Entering 'PDB' will only search sequences with a corresponding PDB entry whereas entering 'GenBankNR' will search all known protein sequences available from GenBank
(non-redundant division). Note: GenBank searches take substantially longer than PDB searches.
- Finally, press the 'Search DB' button. The progress will be printed out in the status window, and when the search is done the results will be emailed to you.
Note: You must keep your browser and this java applet open and active until the search is completed or the search will be terminated (i.e. do not put your computer in sleep or hibernation mode, it must remain on with an active internet connection).
Page last updated by email@example.com 10/24/2011.