Last Science Chat of 2015

The year is disappearing fast and it is time to announce the last science chat of the year. Mark your calendars and set your clocks for this, because we are having a chat on a different day of the week: a Friday!

The Date: 13 November 2015 (Friday) Add your questions to this post! If you don't have a question yet? Bookmark this post and add them closer to the event.

Science/development feature suggestions? Try the forum for feedback first on your idea from other players. Science related bug? Post it in the puzzle comments or steps to reproduce in feedback - or at minimum, operating system, puzzle number and any error messages you're seeing!

The location: #veteran, IRC (Get help with chat here.)
The Time: - 20:30 - 22:00 GMT (we are allocating approximately 1.5 hours, as it is the last chat of the year and a long way til January) GMT (aka 12:30-14:00 PT)
The Time Zone Converter: Right this way!
The Topics: Science chat!

Looking for inspiration? Follow-up on previous topics? Read our previous chats.

We can't wait to see you there.

(Mon, 10/26/2015 - 15:36  |  9 comments)
Joined: 05/19/2009
Groups: Contenders
Efficiency suggestions for the chat

- Please provide training for upcoming drug design puzzles so we will not lose a lot of time learning how to swim when the time is there.

- fixing some of the bugs that cause scoring issues with hbonds, thus influencing science results.

- What will be your agenda for the announcements / discussions ? Please post here so we can already read about it in advance and already think of questions we might have.

- Please prepare your answers for the questions that were asked here so you will spend less time typing those answers online and thus have more time to respond to ad-hoc follow-ups. I notice there is a lot of time spent in typing the answers during chat on questions that were asked in the thread beforehand.

Joined: 04/24/2014
Groups: None
Thanks!

Thanks for your candid feedback about the chat itself (and the added suggestions), we always appreciate the input! We know the hbonds issues are annoying, and we continue to do our best to keep at fixing things in a timely fashion - we appreciate everyone's patience with that, as we are, as always, a small team. (And if it's one thing I've learned, sometimes what looks like a "fast fix" is often dependent on other fixes.. which makes it not so fast.)

With regards to "training", I am assured by our drug design side of the team that they want to give as much information as possible to make these puzzles a success, so as we continue to work out the quirks that have prevented them from appearing as soon as hoped - hang in there! It's on the list.

Fortunately, every single chat within the last year or so seems to fall into a standard pattern (you can all let me know if we've deviated too far off the formula):
- Greetings/Housekeeping
- Updates from the team as needed
- Posted questions first (we try to group them together by subject, so we can keep things from jumping around too much)
- ad-hoc questions directly related to the answers (we try to limit those to 2-3 to keep things moving)
- Open questions next

...so that might help you a bit. This general outline keeps our team on track (mostly me), and everyone with a general idea of what to expect. So really, the agenda gets set by what gets asked in this, the official chat thread, and you, by which I mean the community. :)

While we have thought about typing a lot of answers in advance - the team usually preps key points they want to hit in advance based on the questions in the chat thread, but we've ultimately elected for a more interactive approach from the team, as often multiple members of the team will want to chime in with different perspectives/information on the same topic or question. (Otherwise we'd just take questions and write a blog post! Not as fun for everyone.) :) That being said, I'm always looking for a way to help streamline and make things more efficient to keep our limited time from descending into chaotic jumbles where questions don't get addressed properly. It's a work in progress, and things are likely to be fine tuned over time.

Hope that helps - I wanted to make sure that as you take the time to put these thoughts down that I also took some time to address them for you, and thanks for the input!

Joined: 09/24/2012
Groups: Go Science
Polymers

In the case of proteins in multiple parts (dimers, trimers, or like in the latest HIV puzzle: a piece that can go out in the solution and come back).

I understand that each monomer (or piece?) should be stable alone in a solution: Sufficient number of hydrophobic outside (except if the solution is oily like in a recent contact puzzle...).

Does it mean that we should regularilly "test" or current solution by separating the monomers and verify that it's still stable enough as monomers?

Personally, I try to start with a good monomer before to join them in the complex. But once it's in the complex, mutations may favor hydrophobics in the interface: not sure that my monomers of ultimate solution are still stables enough if alone in water.

Joined: 09/24/2012
Groups: Go Science
ED and contact: outside the cloud

I understood that for contact and ED puzzles, there is something "outside the cloud" like:

-contacts to another clone protein (that gives us "contacts", for example, from bottom of the protein to it's top).

-density bonus outside of the cloud (because the cloud repeats itself to infinite? Is it the case for the latest ED puzzle?)

Is it due to real measurement conditions where many copies of the protein are in solution? So that the measured ED is in practice "infinite", repeated many times.

If it is the case: How can you present us a single protein? How do you decide to cut the all cloud right on a unique protein? (and not 2 half proteins for example). Is there a risk that we are asked to work on an erroneous piece made of 2 or 3 pieces of protein?

Joined: 09/24/2012
Groups: Go Science
A simple question

For the latest ED puzzle, it's said that crystallographers found the structure.

Do you have an idea of the time and/or number Full Time Equivalent was needed for this success? Is it a hard semi-manual "hand-folding" (as asked to the students) or is it only making a lot of crystals and let some computer calculate thinks?

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Joined: 10/02/2011
V3 hairpin

On the recent V3 hairpin puzzle, what is the potential benefit of mutating the hairpin to make it more rigid? I assume we can't convince the HIV to use our designed sequence in place of its usual one?

Susume's picture
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Joined: 10/02/2011
VEGF receptor 1

In the July chat blivens reported that this project (including a foldit result) was being written up for publication. Any estimated timeline for when the results might be published?

Madde's picture
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Joined: 05/29/2008
Groups: Void Crushers
And now for something completely different

This is something I was wondering for ages and has nothing to do with any current or previous puzzles:

In opposition to proteases, are there also "glue" proteins or are they even thinkable? By that I mean proteins that could join the C- and N-termini of different proteins or even the very same one, forming a ring.

Joined: 04/24/2014
Groups: None
Bring your questions to our "open section" of chat!

We're closing the posted question section for now - we only have about 45 minutes until chat time, so save those questions up and be ready to ask at the end of the chat!

Please do keep them short and simple - we want everyone who has questions to have a great opportunity to ask!

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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