10 Search Suggestions for the PDB
I previously mentioned the Protein Data Bank (PDB). In brief, it is the world wide depository of macromolecular structures. Currently, 150,000 scientists from more than 150 countries visit the PDB each month. I am grateful that the PDB is freely available as it has served as an invaluable resource. A number of items have come to mind regarding the search feature in the PDB. I do not have the background to properly gauge the feasibility of these 10 search improvements, so please think of the following as a wish list rather than demands.
1) Eliminate the need for pop-up windows
-most browsers block pop-up windows, making these searches mildly annoying.
2) Have an option to simplify the results
-such as eliminating the images of the proteins (faster loading)
-reduced space would allow for more macromolecules to be displayed on each page (perhaps allowing 15 macromolecules to be shown, rather than 10)
3) List residues that are not within electron densities as a percentage
-residues at the termini or in flexible loops may not be within the electron density, however this may not be noticed by researchers who are unfamiliar with crystallographic models
-by seeing a percentage, a researcher may become aware that he or she should be examining the coordinate file with the electron density (like that which can be generated using the electron density server)
4) Eliminate separate ‘Evaluate Subquery’ toggles
-so it resembles a Google search
5) Save the original search
-it is frustrating having to toggle 5 ‘Evaluate Subquery’ entries and then, should you want to adjust one, have to completely re-enter all of them.
6) Provide an entry of when the structure factors will be available on the structure summary page
7) Ability to automatically load the structure factors with electron density
-similar to what can be done using the electron density server
Be able to search using metals
-instead of using a separate database
9) Be able to receive an email notification if/when a structure is deposited by a colleague
-this will allow you to monitor labs that are working on similar projects
-you’ll know when to send a colleague an ‘even a blind squirrel will eventually find a nut’ note
10) Have a ‘Find Related Articles’ button
-if applicable, auto enter the title of the article into Hubmed
Andreas
December 29th, 2009 at 11:28 AM #
Hi Sean,
The RCSB PDB web site has been going through major changes over the last year and the user interface has been greatly improved. As such some of your comments probably should be re-visited now.
2) Search results are displayed quite differently now. Besides the standard results view, you can display pre-generated reports or create custom reports and there are many other options like downloads, filtering of proteins with high sequence similarity, etc.
4) Looks quite different in the new interface.
5) The left hand “Search” box allows you also to modify or refine a query. Every query can be stored in MyPDB.
9) MyPDB also allows you to store queries and receive email notifications when new structures are found that match your query.
10) There is a new “Literature” tab that provides access to open access literature that is related to a PDB id. http://www.rcsb.org/pdb/explore/literature.do?structureId=1HIV
Sean
December 31st, 2009 at 8:04 PM #
Hi Andreas,
Love the updates! Keep up the great work!