Science Chat: This Week!

scichat.pngIt's time for our first science chat of 2016!

Things we're likely - but not entirely guaranteed - to talk about:
VEGFR update
Drug Design Updates
An update on the UMichigan challenge
Upcoming puzzles/themes (More Marburg? Ebola? Some other disease?)

The Date: 14 January 2016 (Thursday)
The location: #veteran, IRC (Get help with chat here.)
The Time: 1930-2030 (or so, but the official chat ends after an hour) GMT (aka 1230-1330 PT)
The Time Zone Converter: Right this way!

Please post your questions in this thread to get priority in the queue.

(Wed, 01/06/2016 - 16:42  |  8 comments)
Susume's picture
User offline. Last seen 6 days 16 hours ago. Offline
Joined: 10/02/2011
Buried tyrosine and tryptophan

All these years I have thought burying the large hydrophobics was important. But bkoep's hydrogen bond network video says it is unfavorable to have a tryp or tyr buried where it can't make a hydrogen bond. Should we be putting these large hydrophobes at the surface (or where the surface meets the interior) so they can bond with water?

frood66's picture
User offline. Last seen 15 weeks 6 days ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
I think many would be

I think many would be interested to hear more info about these two - they certainly fascinate me. I guess foldit is not capable of some scoring issues with them - but understanding them better would be great.

Joined: 09/24/2012
Groups: Go Science
Residues scoring too low

I just wonder why some residues should not score "too low" in filters, and how much is this "too low". Is that a general rule, including for de-novo?

Susume's picture
User offline. Last seen 6 days 16 hours ago. Offline
Joined: 10/02/2011
Grids in drug design

What are the grids in the drug design interface for?

spvincent's picture
User offline. Last seen 4 hours 38 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Design puzzle parallelism

A lot of solutions to design puzzles have the structural elements parallel to one another or nearly so. It's a very natural thing to do and the structures are often relatively easy to make and score well. Yet most proteins in nature don't fold this way. Still perhaps this is one of the things you're looking for: proteins that fold into shapes that nature hasn't found much use for. The goals in design puzzles have always seemed a little vague: some guidance here would be useful.

bertro's picture
User offline. Last seen 1 year 1 week ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
De-novo's origin

Where are the current De-novos coming from and why are we doing them?

bertro's picture
User offline. Last seen 1 year 1 week ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Are we going to have more ED puzzles?

Are we going to have more ED puzzles?

and if yes, can ED get some improvements and/or answers:

https://fold.it/portal/node/2001368

Joined: 09/24/2012
Groups: Go Science
Do you still record script use?

-or succession of commands or actions used for a top solution?
-are the scripts still of any help for Roseta algorythm ?
(for some puzzle types like revisiting, it's nearly possible to find a top solution only with scripts)

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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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