Predicting the functional consequences of point mutations in proteins.

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

For faster processing, PACKPRED 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. How to specify the position(s) to mutate?
Format specification help, please see Format help.
Q. Are there any worked out examples to help me understand the output of packpred ?
Yes, there are. Please see the Examples page
Q. How to solve and interpret different warning messages shown by the server ?

  • 'Missing atom(s) in the PDB structure': What does it mean and how to solve it ?


    This means that there are missing atom(s) in some of the amino acid residue(s) in the structure specified by you. To rectify this, you need to model the missing atoms. There are several tools to model the missing atom(s), for ex. modeller. You can re-submit the structure after modeling the missing atom(s).

    This will not stop the job from running but missing atom(s) can affect the calculation of atom and residue depths so you should always model the missing atoms before submitting your structure for processing.

    You will be notified about the missing atom(s) whenever the program finds them.

  • 'Non-Standard residues found' : What does it means and how to solve it


    It simply means that the structure contain some non-standard amino acid residue(s), for ex. Nor-Leucine, selenocysteine and selenomethionine etc. The program will not stop because of this. However, these residues will simply be ignored by the program. You will be notified about such residues whenever the program find them.
    • 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 PACKPRED. We suggest that you download the structure from the PDB database and upload it.

  • Error message: Main Chain identifier not found


    This error means that while extracting the PDB structure from the database, PACKPRED was unable to find the particular main chain identifier in the PDB.

    Example:
    Input: 1TIG,F
    PACKPRED will try to extract all the amino acid residues in the main chain 'F' of the PDB structure, if it can not find the chain identifier ('F') then the above error will be shown.

  • Error message: Residue not found


    It means that while extracting the specific amino acid residues from the PDB structure, PACKPRED was unable to find the mentioned residue(s).

    Example:
    Input: 1TIG,A:D84L
    PACKPRED will first check if residue 'L (Leucine)' and 'D (Aspartic acid)' are present in main chain 'A' of PDB 1TIG, if not then it will show the above error.

  • Error message: Residue position absent


    It means that one or all of the residue position(s) mentioned by the user are absent.

    Example:
    Input: 1TIG,A:83
    If there is no residue position '84' in chain 'A' then the above error will be shown.

  • Error message: Residue not found at the specified position


    it means that the residue is not present at the specified position in the PDB file.

    Example:
    Input: 1TIG,A:D83L
    If there is no residue position 'D (Aspartic acid)' at position '83' in chain 'A' then the above error will be shown.

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

    ' symbol on the extreme right hand side of the Packpred main pages. This will start an automated tour of the Packpred 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.