Finding your way with PDBe searches

Image to highlight the search improvements at PDBe
01 June 2018

You might have noticed some changes on the PDBe website recently as we’ve introduced some great improvements to the search options. We hope that these will help you find exactly what you are looking for in the PDB archive. Improvements include the addition of protein sequence searching, many more search terms, an upgraded interface and the ability to input more advanced search queries.

 

Sequence searching

We have implemented sequence searching of proteins in the PDB archive using the pHMMER tool created by our colleagues here at EMBL-EBI. Using our ‘Advanced search’ option, you can input a protein sequence and find molecules in the PDB based on their similarity to that sequence. This will be a particularly useful tool to enable researchers with a protein sequence background to begin exploring the possibilities of the PDB archive.

Image highlighting sequence search results at PDBe 

A more advanced search (with EM data)

We have added loads of new categories to our search, including a host of electron microscopy specific search fields, enabling you to explore EM-derived data based on experimental methods and equipment used.

We have wrapped all of this up into our advanced search form that allows you to ask more complicated questions in your search queries. For instance, you could search for all molecules classified as TIM barrel structural domains, within a resolution range of 1 to 1.5 Angstrom, where data were collected using a pixel detector and excluding specific unit cell dimensions. We hope that this will vastly improve your experience of searching for macromolecular structures at the PDBe.

 

Structure visualisation without leaving the search page

Our LiteMol structure viewer has been integrated into the search results page, enabling you to view a particular structure instantly at the click of a button. Just select the ‘3D visualisation’ option on a particular search result and the LiteMol viewer pops up, giving you the chance to view the 3D structure and (if available) the associated experimental data.

We hope you find the new search pages useful, but if you have any problems or suggestions, then please let us know. Either hit the feedback button on any PDBe webpage or email us at pdbehelp@ebi.ac.uk. We aim to create the best service we can for our users and always appreciate your help in making that possible.