P212121

PDBalert is a free web-based automatic system that alerts users as soon as a PDB structure with homology to a protein of interest becomes available. Users need to simply upload their personal protein sequences of interest. Once a week, when new proteins are released to the PDB database (on Wednesdays) even if they are on hold, PDBalert compares the new structures with the users’ sequence(s). When a significant match is found, the user is alerted by an email containing a link to the search results. Reminder: have your protein sequence(s) of interest ready when registering.

Why is this application helpful to a crystallographer?

This web application will automatically email you if a protein related to one of your current projects has been deposited in the PDB. PDBalert removes the need to regularly check the new PDB entries and will also highlight relationships that are more distant than what would appear by using the simple key word search in the PDB. This information could help you with phasing via molecular replacement or let you know if you have been scooped.

How is the search performed?

The search is done using the HHpred, which is a remote homology detection server (reference). A pairwise comparision is performed using a profile Hidden Markov Models (HMMs) (reference).

One drawback maybe that you have to register to use this web application. However, since they need to email you if a PDB is deposited of similar sequence then it makes sense that they need some sort of registration process.

The PDBalert system was developed at the Gene Center of the University of Munich. The most recent publication on PDBalert can be found here in pdf format.

As a side note it is nice to see some programs related to crystallography using Ruby instead of Fortran.

How can I quickly find an annotated sequence of my protein?

Try using Pfam 23.0

Click on ‘VIEW A STRUCTURE’
Enter the PDB code (if you would like to simply test this without a code, you can click on ‘example’)
Click on ‘Sequence mapping’

Click on the link under ‘UniProt ID’
This will take you to the UniProt summary page.
To get all the information about your protein of interest.
You will see the following and click on the id (see below).
This is the summary of UniProt entry ‘CLICK ID”

General or sequence annotation information and scan the references.

Why is this tool great?

1) It will save time by taking advantage of the PDB ID which you probably already have
2) UniPort searches both Swiss-Prot and TrEMBL (so you don’t have too)

You can find out more information about Uniport here.