How To Get Dimer Proteins?

Question

[rasaq]

Hello,

I would like to get a data set of dimer proteins. How can I get dimer proteins from scop? What would be the easiest way to download dimer proteins?

Your suggestions woud be appreciated!

Answer 1

[João Rodrigues]

Depends what you want to do with them. You could use 3DComplex (maybe easier than SCOP) or just google for protein docking benchmark.

Answer 2

[Neilfws]

SCOP is primarily a database of protein folds and so is not especially useful in this case.

The "easiest way" is to use PDB advanced search. Let's say you want (1) only protein chains and (2) proteins thought to be dimeric in their native ("biological") state. You would select:

1. Macromolecule Type -> Contains Protein -> Yes; then choose "No" for the other options
2. Add Search Criteria -> Structure Features -> Number of Chains (Biological Assembly) -> between 2 and 2

Click "Result Count" - currently returns 29 690 entries.

Then "Submit Query" - you may want to remove entries at a certain level of redundancy (select level and check box before submit).

You can then download what you want (e.g. PDB IDs, PDB files) from the results page.

[rasaq]

Great!! Nice explanation. Thank you so much.

[Neilfws]

No problem. Votes are appreciated ;)