Database Selection
Currently, users can search over following structural databases:
Serial no. Database
1 non-redundant (90% sequence identity) set of 24,563 protein chains
2 non-redundant set of 3468 human protein chains
3 a set of 2262 DNA-protein complexes
4 non-redundant set of 493 RNA
5 non-redundant set of 1368 DNA

Uploading your own database:

The server offers the flexibility of uploading your own database, should the default ones be inadequate for your queries. The user should upload a plain/ASCII text file. The format of the file is as follows:

The first line is the type of the database (protein/DNA/RNA or DNA-protein) and next lines are just the 4 letter PDB code and/or chain - for example:

Sample file for user uploaded database

protein
7odcA
4eetB
3mhpC
3c4s
1xak
3l32

Choosing the number of hits for database search
Number of hits for database search
  • As databases could be large, you may want to restrict the number of comparisons for which you may require detailed information (alignment files and the superimposed structures). The hits are ranked according to Z-scores.
  • Email Notification
    We advise users of long running jobs to fill in this field so that they could be notified (with a link to their results) on job completion. We will neither store nor disseminate these e-mail addresses.

  • If no email address is provided: Please save the URL that is shown after you submit the job. You can either leave the page to refresh until completion or bookmark it for later. Once the job finishes, result page referred by the URL will show the results.
  • Run Time Approximation
    The runtime for a job usually increase with an increase in the following:
  • 1. Size of the query structure.
  • 2. Size of database.
  • 3. Number of representative atoms.
  • 4. Number of best matched cliques for each alignment.
  • Note: The reported run times were calculated when the system was idle (no other resource intensive operation was running on the system). The run time may vary for a new database search depending on the system load and rank of your job in the queue. If the job is in queue then the waiting time in the queue will be added to the standard runtime of the job.
    Approximate runtime estimate for searching 'Protein database' (24,563 PDB chains, NR 90)
    PDB Code Size Runtime in hours
    5CFH 100 residues 13 hours
    1A3H 300 residues 13 hours
    5EJY 500 residues 18.5 hours
    Approximate runtime estimate for searching 'Human Protein database' (3468 PDB chains, NR 90)
    PDB Code Size Runtime in hours
    5CFH 100 residues 1.5 hours
    1A3H 300 residues 2.5 hours
    5EJY 500 residues 3 hours
    Approximate runtime estimate for searching 'DNA Protein complex' database (2262 PDB)
    PDB Code Size Runtime in hours
    1AN2 86 residues 1 hour 7 minutes
    4Z6C 335 residues 1 hour 20 minutes
    5D9Y 462 residues 1 hour 45 minutes
    Approximate runtime estimate for searching 'RNA' database (493 PDB, NR 90)
    PDB Code Size Runtime in hours
    5KVJ 32 residues 15 minutes
    3RGJ 172 residues 17 minutes