Currently, users can search over following structural databases:

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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

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.

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.

The runtime for a job usually increase with an increase in the following:
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.

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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