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Message boards : News : Science non-stop: another paper, another badge

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Toni
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Message 52244 - Posted: 13 Jul 2019 | 8:36:59 UTC
Last modified: 13 Jul 2019 | 9:08:27 UTC

...and here's another badge for another publication issued in 2018, Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. This one is also on Sci. Rep., open access.

Here, the authors used Gpugrid-based simulations to reconcile experimental results on Dopamine D3 receptor antagonists with their molecular structures. They used the large-scale high-throughput molecular dynamics with Markov state models (MSMs) to determine an alternative and possibly elusive pose ("cryptic") consistent with the mutation data.

Thanks to every contributor!


Noelia Ferruz, Stefan Doerr, Michelle A. Vanase-Frawley, Yaozhong Zou, Xiaomin Chen, Eric S. Marr, Robin T. Nelson, Bethany L. Kormos, Travis T. Wager, Xinjun Hou, Anabella Villalobos, Simone Sciabola & Gianni De Fabritiis
Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs
Scientific Reportsvolume 8, Article number: 897 (2018)

The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments. We overcame the limitations of static docking by using large-scale high-throughput molecular dynamics (MD) simulations and Markov state models (MSMs) to determine an alternative pose consistent with the mutation data. The new pose maintains critical interactions observed in the D3R/eticlopride X-ray crystal structure and suggests that a cryptic pocket forms due to the shift of a highly conserved residue, F6.52. Our study highlights the importance of GPCR dynamics to understand ligand binding and provides new opportunities for drug discovery.

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Profile Retvari Zoltan
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Message 52247 - Posted: 13 Jul 2019 | 22:30:42 UTC - in response to Message 52244.

Wow!
Two badges in a week, that's awesome!
Can you publish the top 20 like before?

PappaLitto
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Message 52248 - Posted: 14 Jul 2019 | 0:58:32 UTC

I haven't gotten a single badge from 2018, did I not contribute to these studies?

Profile tito
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Message 52250 - Posted: 14 Jul 2019 | 6:39:03 UTC - in response to Message 52248.

Where are those new badges, as I can not find ANYONE with them?

Profile Michael H.W. Weber
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Message 52252 - Posted: 14 Jul 2019 | 7:40:04 UTC - in response to Message 52250.
Last modified: 14 Jul 2019 | 7:40:27 UTC

http://www.gpugrid.net/forum_thread.php?id=4606&nowrap=true#52251

Where are those new badges, as I can not find ANYONE with them?

Well, Zoltan got the Ferruz badge.

Strangely, when clicking on his badge icon in the signature, the cancer project webseite opens but the paper isn't listed there...

Michael.
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[CSF] Thomas H.V. Dupont
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Message 52254 - Posted: 14 Jul 2019 | 8:57:04 UTC

Thanks again, Toni!
Unfortunately, many publications are missing in the dedicated pages (not only this one), Michael.
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JoergF
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Message 52255 - Posted: 14 Jul 2019 | 9:18:27 UTC - in response to Message 52248.

I haven't gotten a single badge from 2018, did I not contribute to these studies?


same here...
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Toni
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Message 52257 - Posted: 14 Jul 2019 | 10:46:13 UTC - in response to Message 52255.

Here is the list for the paper above. There were relatively few WUs so probably not everyone got them.
I confirm that they are missing from the website (which requires more manual updates).

rank userid credit
1 25378 83460000
2 1084 69270000
3 93201 63660000
4 100499 62400000
5 14310 59310000
6 109388 52680000
7 101936 45450000
8 102086 40860000
9 101769 36360000
10 69336 32700000
11 73475 30540000
12 63403 29280000
13 97627 26760000
14 126468 25980000
15 9991 25890000
16 85852 25740000
17 28899 25440000
18 64884 22710000
19 31053 21060000
20 19626 20880000

kain
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Message 52258 - Posted: 14 Jul 2019 | 10:46:53 UTC - in response to Message 52250.

Where are those new badges, as I can not find ANYONE with them?


I have mine :)

Bedrich Hajek
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Message 52260 - Posted: 14 Jul 2019 | 13:16:04 UTC

Since Noelia Ferruz is the principal on this paper, and she was with this project from 2011 to 2015. Would it be safe to assume that all crunching for this paper was done at that time?







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Message 52262 - Posted: 14 Jul 2019 | 17:50:41 UTC

Thanks for the badges,keep the work going!

[CSF] Thomas H.V. Dupont
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Message 52278 - Posted: 16 Jul 2019 | 6:06:40 UTC - in response to Message 52257.

Here is the list for the paper above. There were relatively few WUs so probably not everyone got them.
I confirm that they are missing from the website (which requires more manual updates).

rank userid credit
1 25378 83460000
2 1084 69270000
3 93201 63660000
4 100499 62400000
5 14310 59310000
6 109388 52680000
7 101936 45450000
8 102086 40860000
9 101769 36360000
10 69336 32700000
11 73475 30540000
12 63403 29280000
13 97627 26760000
14 126468 25980000
15 9991 25890000
16 85852 25740000
17 28899 25440000
18 64884 22710000
19 31053 21060000
20 19626 20880000

Thanks Toni!
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[CSF] Thomas H.V. Dupont
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www.crunchersansfrontieres.org

Profile Retvari Zoltan
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Message 52280 - Posted: 16 Jul 2019 | 10:49:38 UTC - in response to Message 52257.

Here is the list for the paper above. There were relatively few WUs so probably not everyone got them.
I confirm that they are missing from the website (which requires more manual updates).

rank | ---credits--- | user
_1__| 83,460,000 | Stoneageman
_2__| 69,270,000 | Roald
_3__| 63,660,000 | RaymondFO*
_4__| 62,400,000 | jjch
_5__| 59,310,000 | Retvari Zoltan
_6__| 52,680,000 | caffeineyellow5
_7__| 45,450,000 | Rion Family
_8__| 40,860,000 | Orange_1050
_9__| 36,360,000 | Acey Pilot
10__| 32,700,000 | neilp62
11__| 30,540,000 | Viktor Svantner
12__| 29,280,000 | Venec
13__| 26,760,000 | Mel S Stark
14__| 25,980,000 | Gunde
15__| 25,890,000 | Beyond
16__| 25,740,000 | Brian Stansbury
17__| 25,440,000 | Bob Deller
18__| 22,710,000 | Nikke
19__| 21,060,000 | Thomas M. Taylor
20__| 20,880,000 | Bedrich Hajek

I've made the toplist human readable.
I hope I've corrected all typos.

[CSF] Thomas H.V. Dupont
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Message 52289 - Posted: 17 Jul 2019 | 5:09:17 UTC - in response to Message 52280.

Thanks Zoltan and congrats for your 5th place!
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Message 52506 - Posted: 14 Aug 2019 | 17:09:46 UTC

I don't understand on my example how it is possible to score over 200M credits and never get a badge, while according to the table sometimes 20M is enough =(

PappaLitto
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Message 52507 - Posted: 14 Aug 2019 | 18:35:45 UTC - in response to Message 52506.

I don't understand on my example how it is possible to score over 200M credits and never get a badge, while according to the table sometimes 20M is enough =(

You should at least get a white badge if you contributed at all. I too am missing a few badges, I think it's just down to whether or not the scientists get around to manually assign badges.

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Message 52508 - Posted: 14 Aug 2019 | 20:06:48 UTC - in response to Message 52507.

... I think it's just down to whether or not the scientists get around to manually assign badges.

you are serious?

PappaLitto
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Message 52509 - Posted: 14 Aug 2019 | 20:16:17 UTC
Last modified: 14 Aug 2019 | 20:16:38 UTC

If it's not that, why would people that have definitely contributed to every study since 2016 like myself, not have any studies in 2018?

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Message 52517 - Posted: 17 Aug 2019 | 12:26:23 UTC - in response to Message 52506.

I don't understand on my example how it is possible to score over 200M credits and never get a badge, while according to the table sometimes 20M is enough =(


None here either.

Guess I wasn't running the project during those specific times.

Some the studies seemed short based on the credit for the top donors.

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Message 52518 - Posted: 20 Aug 2019 | 23:47:42 UTC - in response to Message 52506.

I don't understand on my example how it is possible to score over 200M credits and never get a badge, while according to the table sometimes 20M is enough =(

The best I can tell, you don't get any badge before the paper on that part of the project is published.

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Message boards : News : Science non-stop: another paper, another badge