Protein Interaction Z-Score Assessment (PIZSA)

Q. How is the PDB database stored and used by PIZSA. How regularly is the database updated ?
Q.1(a) Database location

For faster processing, PIZSA uses a locally stored copy of the PDB database. This is done to avoid fetching the structures from remote PDB database and hence save time.
Q.1(b) What is the frequency of updating the local database ?

The local copy of the database is synchronized with the latest snapshot of the PDB database every week (on Sunday at 01:30 AM, Indian Time Zone). Due to the 1 week window between successive update of the local database, sometimes, it can happen that the PDB code entered by the user is not found by the server and the server will show an error saying that the 'PDB structure not found'
Solution

If you are sure that you have entered a correct a PDB code but the server is still reporting the 'PDB structure not found' error, then we suggest that you upload the structure. This can happen when the local copy of the database is yet to be synchronized with the remote server.
Q. You want to do alanine scanning or saturated mutagenesis on a specific list of residues ?
Mutate a given list of residues to every other residue

You will need to upload a text file that specifies the details in specific format, a sample of the file and format is here

Mutagenesis input file format: Each residue to be mutated is represented in the following format on a separate file.

XXX:YYY:A, where XXX = residue number, YYY = residue type & A = protein subunit.

For example - 321:ALA:A is the Alanine at position 321 of the subunit A

Format specification help, please see Format help.
Q. Are there any worked out examples to help me understand the output of pizsa ?
Yes, there are. Please see the Examples page
Q. How to solve and interpret different types of errors shown by the server ?
Below is a description of the most frequent types of errors and warnings shown by the server,

  • Error message: PDB structure not found


    This error means that the PDB structure specified by the user does not exist in the local copy of the PDB database. This error will not be reported this error for uploaded PDB structures. If you have entered a correct 4 letter PDB code then it means that the local copy of the PDB database do not have that specific structure.

    Solution: If the structure entered by the user is recent (less than 1 week old) then it may not exist locally in PIZSA. We suggest that you download the structure from the PDB database and upload it.

  • Error message: PDB structure is not a complex


    A valid PDB complex must contain at-least two subunits or chains. Examples of valid PDB complex are 4PZA, 1GZX etc.

    • Q. How to use the web server ?
    It's very easy. Just click on the '

    ' symbol on the extreme right hand side of the Pizsa main pages. This will start an automated tour of the Pizsa server. You can forward, pause or rewind the tour whenever you want.
    Q. You have a question/doubt that is not addressed in the above list.
    Please contact us regarding your query by sending an email at Contact us.