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

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

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

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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President of Rechenkraft.net - Germany's first and largest distributed computing organization.

Thanks again, Toni!
Unfortunately, many publications are missing in the dedicated pages (not only this one), Michael.

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[CSF] Thomas H.V. Dupont
Founder of the team CRUNCHERS SANS FRONTIERES 2.0
www.crunchersansfrontieres

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

same here...

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I would love to see HCF1 protein folding and interaction simulations to help my little boy... someday.

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

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

I have mine :)

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?

Thanks for the badges,keep the work going!

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
Founder of the team CRUNCHERS SANS FRONTIERES 2.0
www.crunchersansfrontieres

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.

Thanks Zoltan and congrats for your 5th place!

---

[CSF] Thomas H.V. Dupont
Founder of the team CRUNCHERS SANS FRONTIERES 2.0
www.crunchersansfrontieres

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 =(

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.

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

you are serious?

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?

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.

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.