Why is the exact PDB entry sequence important with the Electron Density Refinement puzzles ?

Started by Bletchley Park

Bletchley Park Lv 1

Can someone (@LociOiling and @beta_helix ) please explain why it is relevant to know the sequence and the precise PDB entry ? I see many comments under these puzzles and wonder what their purpose is.

rmoretti Staff Lv 1

I don't think you should need to know anything additional about the structure in order to do well on the puzzle and to meaningfully contribute to the science.

That said, I'm sure some people are interested in additional details about the system being studied. (What is this protein we're working on? What is it used for? Why is it interesting?) Knowing the sequence and the PDB code of the protein could allow you to do additional research into things. You can do database searches and look up research papers and the like, if you're so inclined.

There's also a possibility that some of that research will lead to some insight that changes how you approach the puzzle. For example, you might look up the structures of similar proteins, and look at what sort of features they have. This might lead you to an idea about how you can change the structure to be better. – That's a bit of a long-shot, and you don't necessarily need to do that to find a decently scoring structure, but it's the sort of thing a professional structural biologist might do, and having the sequence and PDB code makes it slightly easier.

LociOiling Lv 1

A lot of things in Foldit are kind of mysterious. Looking up the proteins for the ED Recon puzzles is a way to clear up some of the mystery.

On the practical side, in the earlier ED Recon puzzles, there were a lot of problems with "puckers". Puckers occur when a Foldit puzzle incorrectly connects the sides of a missing residue gap. That's really what started my interest in looking up the ED Recon proteins. We now have a recipe to detect a pucker (one slipped through recently, hence 2672b), and a better way for recipes to detect chains.

(I'd also note that puzzle 2460, PDB 7CTO, had a pucker, and despite that, now has a Foldit entry in PDB-REDO. It was only a small pucker in a large protein.)

Otherwise, it's just interesting to know more about what we're looking at. For example, this week's puzzle 2675 has DNA, and that's apparently because the protein is an enzyme that works on DNA, a DNA polymerase. Good to know, but maybe not very helpful in solving the puzzle. As mentioned in my comments, there are several hundred PDB entries for the 2675 protein, and it's not clear which one corresponds to our puzzle. The PDB search tool at rcsb.org isn't too helpful in this regard.

Also in the "good to know" category, PDB entries now include a validation section, which gives a quick visual representation of "problems with the published solution".