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Fri, 2005-12-02 06:03 — marcius

Hi all, We have started the development of projects in the Malaria community. There are several projects that we are starting (see more about the projects here). We would love to see more projects being proposed. Please, use this venue for such a task. We will listen and try to adapt as much as we can your suggestions! If you have a particular comment to make about an existing project, the best way will be to leave a comment in their respective pages.

Thanks and we hope you will participate in the projects!

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Wed, 2005-12-14 05:35 — Ash

Malarial binding sites

Hi Marc & Co. As per your request... I'll sign on, the basic idea is to identify malarial binding sites & develop that as a resource and then start sifting through them, probably others are thinking along the same lines?? We'd want to pull out all the inherited binding sites, discarding any that are too 'common'. One problem is that LigBase isn't working well (at least on my end) and/or needs updating which I'd be happy to do or help with. To that end, I'd need to get access to the scripts (ie an account) or get copies of them to update the site. Let me know if that would be OK. Best, -Ash
Wed, 2005-12-14 17:44 — marcius

Identifying binding sites in Malaria protein structures

Hi Ash!

This type of projects is exactly what we need in TDI!!!

The idea is that somebody (such as you are doing for this proposed project) takes an initial step to accomplish a task. Then the results are posted in TSL/Malaria (in that the TSL people or myself can help) so the community can look at the results and comment on them.

For your particular project I envision the following actions (comments are welcome!)

1. Get all up-to-date info from PDB (all known structures of P. falciparum).
2. Get all up-to-date info from PDB into LigBase(with the help of some of the Sali folks such as Ursula and Andrea).
3. Get all inherited ligands from DBAli corresponding to all P. falciparum entries in PDB
4. Parse all data and collect it into a nice MySQL entry.
5. Merge the data into the so called Gene Cards (of course as part of your project initiative within TDI/TSL). You can see a preview of the Gene Cards here (not yet released)
6. The community (including yourself or your group) may start getting some relevant hits/info from the results. More eyeballs looking a one problem == more progress!

Any comments/suggestions?

Marc

Fri, 2005-12-16 03:11 — Ash

Malarial binding sites

Hey Marc,
    I spoke with Ursula & Andrea, it sounds like a go. I will start parsing the data after I get the tables. I think most of the data is already available, so that's great!!! I have some setting up to do on my end and will also look at the gene cards. I think your inherited binding sites will be a huge help!!! Hopefully, we can get this on the site soon!!
    Ash