July 2023 - Bayesian validation

summary of today's meeting
by Jared Sagendorf 21 Jul '23

21 Jul '23

Thanks everyone for the discussion today! Here's a summary of the meeting: - Today I presented a high-level overview of model representation in the IHM-Dictionary. The slides I showed can be found here: https://docs.google.com/presentation/d/1oQYKRt4-F7HRLWpUIDr9yiuCxffZIjQ1/ed… - Jeff has initiated the process of getting a Slack channel set up - Joe Courtney will act as coordinator on the UConn side, I'll coordinate on the UCSF/Rutgers side - Hamid will tentatively present some material on Bayesian analysis next meeting, which hopefully can be related to future directions for IHM-Dictionary/PDB-Dev and the PDB proper! - Follow up on discussion for an in-person meeting, potentially later this year. Our next joint meeting is 08/18. See you all then! - Jared

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new PDBe tool on protein conformational states
by Jared Sagendorf 19 Jul '23

19 Jul '23

Hi all, check out this announcement from PDBe on protein conformation comparison: https://www.ebi.ac.uk/pdbe/news/illuminating-protein-conformational-landsca… This is relevant to our current discussion on terminology, which in my opinion is about more than just words, since terminology is a reflection of ones underlying conceptual framework. For our joint meeting with Jeff Hoch's group this Friday, I'll present a brief summary of their work, and I'd also like to present a summary of the current IHM-Dictionary definitions. It'd be good to come prepared to contribute! - Jared

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Re: Next meeting agenda
by Jared Sagendorf 12 Jul '23

12 Jul '23

Sure Jeff, pushing it forward two hours to 12:00 PST should work for most of us. Hopefully that makes it easier for you! I'll update the calendar event on our side. Congrats on the R24! See you Friday, - Jared On Wed, Jun 21, 2023 at 12:20 PM Hoch,Jeffrey <hoch(a)uchc.edu> wrote: > Hi Jared – met too! I added a term to the dictionary . Yulia, Michael > and I will be driving back from a Gordon Conference in Vermont Friday > morning, and it might be tight for us to make the schedule time. I know > there are many schedules to check, but would it be possible to bump the > time back a couple of hours to take some of the stress out? -Jeff > > > > PS – good news is that we heard BMRB will be funded via an R24 mechanism. > Don’t know the budget yet, though. > > > > *From: *Jared Sagendorf <jared.sagendorf(a)rcsb.org> > *Date: *Wednesday, June 21, 2023 at 2:08 PM > *To: *"Hoch,Jeffrey" <hoch(a)uchc.edu> > *Subject: *Next meeting agenda > > > > *** Attention: This is an external email. Use caution responding, opening > attachments or clicking on links. *** > > Hi Jeff, looking forward to the next meeting! > > For the agenda this week, I was thinking we could start with having a look > at some of the terminology, now that we have a dictionary in place. I'll > put together a few slides that I hope will explain the way the Sali group > speaks about modeling, and we can identify if there's any inconsistencies > between the two groups. > > Aside from that, I thought it would be good to begin a discussion on what > the current hurdles are to actually implementing a fully Bayesian > validation pipeline for the PDB. What are the unsolved problems or > unimplemented steps that are missing to actually push this forward, and > could we work together to start solving those issues? > > Also happy to send out any items you would like to bring up! > > > > - Jared >

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