Hands-on: Choosing the best structure for your needs

When deciding on a structure to use to support your research, you may need to consider more than just validation. For example, you may want to consider:

• Structural coverage of the protein chain
• The experimental technique used to determine the structure
• Resolution of the data used to build the model
• Presence of bound small molecules in the structure
• Presence of protein-protein interactions in the structure

Each of the wwPDB partner sites has search functionalities that allow you to fine-tune your search around a selection of these features. All sites allow you to refine your search by molecule name, experimental technique and resolution, while the search results then allow you to see the molecules within the particular structures.

For the following example, we are looking for alcohol dehydrogenase structures solved by X-ray diffraction to a resolution better than 1.5 Angstrom.

In both cases, 3 entries are returned:

The search allows you to further sort these results by other metrics, though the options for sorting differ between the two sites.

• Question 1. Try sorting the search by ‘Entry all residues: more to less’ – this sorts the search so that the top result has the highest coverage. Which entry is given at the top?
• Question 2. Try sorting the search by ‘Quality (desc)’ – this sorts your results by a combination of coverage, resolution and validation score. Which entry is given at the top?

Try changing some of the parameters at each website to specify your own search criteria and sort your results using some of the metrics suggested above. Work out which website works best for you!