PDB export and project aims

Started by ipatrol

ipatrol Lv 1

There are many programs, freely available, that can greatly expedite the process of molecular dynamics modeling. The failure to allow export to a free format combined with the closed-source nature of this crowdsorced operation seems inexcusable. Furthermore, the lack of clarity over the copyright status of our contributions raises serious concerns in regard to the academic philosophy that ostensibly guides this project. This much secrecy is not healthy or beneficial, indeed users have historically proven to be the greatest source of intellectual capital, and allowing more savvy users to try out their own machinations. UW should not try to hoard accolades and credit in the hopes of seizing extra grants. We all enjoy the opportunity to contribute to science, but when pathways are blocked, the most valuable players are likely the first to balk at the restrictions on their own work.

auntdeen Lv 1

ipatrol -

I didn't downrate you but was tempted, just on the basis of your aggressive language. "inexcusable" "ostensibly" "hoard accolades and credit in the hopes of seizing extra grants" - these were not necessary to get your point across.

ipatrol Lv 1

You're missing the point. I don't want access to the client's internals, I want the ability to interface directly with the game using molecular dynamics software. There can be restrictions and limitations, but it ought to be open as an option.

infjamc Lv 1

Note to developers: I've spoken to ipatrol on global chat, so here's further clarification on what's actually being requested.

  1. Ability to export a structure from the game iself to PDB, MDL, etc. The intent is not for research use, but to further refine the structure from the game with a third-party molecular dynamics program.

  2. Likewise, this would require the ability to import the same said format supported in #1.

  3. Part of the difficulty, I think, is finding a way to keep the game fair while allowing exporting/importing solutions. After all, not everyone would have access to molecular dynamics software (or have time to learn them and use them), which could theoretically give some players an unfair advantage. One possible solution I see would be "importing a PDB, etc. makes you an evolver," but even this isn't perfect since it's possible for people to use a third-party program to further refine their own structure.

  4. Ultimately, ipatrol's wish for the long term is to make the project open-source, which has been suggested before ( http://fold.it/portal/node/986352 ). Obviously, such a drastic step would require server-side rescoring of structures to prevent cheating, and most likely the use of more builds than only beta and main (Firefox uses 4 groups, for example).

  5. Regarding the issue of who's going to monitor the latest additions to the code, ipatrol's idea is that trusted editors could be selected (either via a community vote or by approval of the Foldit development team at UW) as a project leader of sorts for delegation purposes.

==> Again, the ideas are his and not mine. I think there's some promise in theory– the hard part is implementing it.

ipatrol Lv 1

Ok, how about let's start with the PDB export. These opaque OPDB files really ought to have some documentation. If they had that, then it wouldn't be hard to whip up a conversion script.

infjamc Lv 1

My impression is that the heart of ipatrol's argument boils down to the following:

"There are other tools out there besides the Rosetta engine that could help with the general goal of protein structure prediction and design. So why not combine the strengths of the different programs by allowing for the possibility of passing the results from one program to another?"

ipatrol Lv 1

I agree, let's focus on that aspect. At the very least, users should be allowed to make their own guides.