Science non-stop: another paper, another badge

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

Author	Message
Toni Volunteer moderator Project administrator Project developer Project tester Project scientist Send message Joined: 9 Dec 08 Posts: 1006 Credit: 5,068,599 RAC: 0 Level Scientific publications	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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Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2343 Credit: 16,206,655,749 RAC: 261,147 Level Scientific publications	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?
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PappaLitto Send message Joined: 21 Mar 16 Posts: 511 Credit: 4,672,242,755 RAC: 0 Level Scientific publications	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?
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tito Send message Joined: 21 May 09 Posts: 22 Credit: 1,730,063,678 RAC: 6,700,549 Level Scientific publications	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?
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Michael H.W. Weber Send message Joined: 9 Feb 16 Posts: 71 Credit: 607,916,391 RAC: 0 Level Scientific publications	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. ____________ President of Rechenkraft.net - Germany's first and largest distributed computing organization.
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[CSF] Thomas H.V. DUPONT Send message Joined: 20 Jul 14 Posts: 732 Credit: 126,845,366 RAC: 190,805 Level Scientific publications	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. ____________ [CSF] Thomas H.V. Dupont Founder of the team CRUNCHERS SANS FRONTIERES 2.0 www.crunchersansfrontieres
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3de64piB5uZAS6SUNt1GFDU9d... Send message Joined: 20 Apr 15 Posts: 285 Credit: 1,102,216,607 RAC: 0 Level Scientific publications	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... ____________ I would love to see HCF1 protein folding and interaction simulations to help my little boy... someday.
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Toni Volunteer moderator Project administrator Project developer Project tester Project scientist Send message Joined: 9 Dec 08 Posts: 1006 Credit: 5,068,599 RAC: 0 Level Scientific publications	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
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kain Send message Joined: 3 Sep 14 Posts: 152 Credit: 823,457,245 RAC: 3,995,286 Level Scientific publications	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 :)
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Bedrich Hajek Send message Joined: 28 Mar 09 Posts: 485 Credit: 11,079,198,466 RAC: 15,660,629 Level Scientific publications	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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Trotador Send message Joined: 25 Mar 12 Posts: 103 Credit: 13,920,977,393 RAC: 9,448,390 Level Scientific publications	Message 52262 - Posted: 14 Jul 2019 \| 17:50:41 UTC
	Thanks for the badges,keep the work going!
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[CSF] Thomas H.V. DUPONT Send message Joined: 20 Jul 14 Posts: 732 Credit: 126,845,366 RAC: 190,805 Level Scientific publications	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! ____________ [CSF] Thomas H.V. Dupont Founder of the team CRUNCHERS SANS FRONTIERES 2.0 www.crunchersansfrontieres
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Retvari Zoltan Send message Joined: 20 Jan 09 Posts: 2343 Credit: 16,206,655,749 RAC: 261,147 Level Scientific publications	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.
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[CSF] Thomas H.V. DUPONT Send message Joined: 20 Jul 14 Posts: 732 Credit: 126,845,366 RAC: 190,805 Level Scientific publications	Message 52289 - Posted: 17 Jul 2019 \| 5:09:17 UTC - in response to Message 52280.
	Thanks Zoltan and congrats for your 5th place! ____________ [CSF] Thomas H.V. Dupont Founder of the team CRUNCHERS SANS FRONTIERES 2.0 www.crunchersansfrontieres
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Diplomat Send message Joined: 1 Sep 10 Posts: 15 Credit: 853,849,648 RAC: 5,979,954 Level Scientific publications	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 =(
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PappaLitto Send message Joined: 21 Mar 16 Posts: 511 Credit: 4,672,242,755 RAC: 0 Level Scientific publications	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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Erich56 Send message Joined: 1 Jan 15 Posts: 1132 Credit: 10,205,482,676 RAC: 29,855,510 Level Scientific publications	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?
	ID: 52508 \| Rating: 0 \| rate: / Reply Quote

PappaLitto Send message Joined: 21 Mar 16 Posts: 511 Credit: 4,672,242,755 RAC: 0 Level Scientific publications	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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mmonnin Send message Joined: 2 Jul 16 Posts: 337 Credit: 7,617,724,223 RAC: 11,001,670 Level Scientific publications	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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robertmiles Send message Joined: 16 Apr 09 Posts: 503 Credit: 755,070,933 RAC: 197,388 Level Scientific publications	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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benefique pour tous Send message Joined: 12 Oct 19 Posts: 1 Credit: 120,776,355 RAC: 0 Level Scientific publications	Message 53619 - Posted: 7 Feb 2020 \| 8:01:06 UTC
	Good for the brain: Raspberry Juice for vitamin B12 and b9 Beef meat for L-Carnitin origin of acetylcholine Fish, almond, fresh vegetable to bring constant choline to the brain Fish especially for phospholipid Such asociated food bring you to increased intelligence Sometimes the benefit of fresh produces of the nature is more important as to look upon bio or not bio Special regards to bio orange for producing orange marmelade self made who has an important activity upon the quality of thinking for the brain I tested each produce and i know yet that the food for intelligence exist in your food shop Guy PFLIEGER
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Pop Piasa Send message Joined: 8 Aug 19 Posts: 252 Credit: 458,054,251 RAC: 0 Level Scientific publications	Message 53620 - Posted: 7 Feb 2020 \| 14:55:11 UTC Last modified: 7 Feb 2020 \| 14:58:04 UTC
	"Badges? We don't need no stinking badges!" (Alfonso Bedoya) True intrinsic satisfaction comes from giving freely rather than receiving copiously. 😉
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Message boards : News : Science non-stop: another paper, another badge

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