Допомога - Пошук - Користувачі - Календар
FightAIDS@home
Розподілені обчислення в Україні | Распределенные вычисления в Украине > Основні проекти розподілених обчислень > World Community Grid
1, 2, 3, 4, 5
mysterix
конечно)
Death
QUOTE
Т.е. 22 мая 2014 года будет побежден СПИД?


22.05.2014 судоку дощитают ))))))

а уж спид потом на освободившихся мощностях )))
Rilian
Project Status, as of November 26, 2012

http://fightaidsathome.scripps.edu/status

Experiment 41: 25% Completed

Experiment 41 involves screening the Enamine library of 2.345 million compounds against the two allosteric sites on the surface of HIV protease. This experiment is similar to Exp. 36, but a different, much larger library of compounds is being screened, and some new targets are being included. The first part of this experiment involves docking compounds against the two allosteric-fragment-bound crystal structures presented in our recent article in Chemical Biology and Drug Design, vol. 75: 257-268 (March 2010). Three other, brand new crystal structures from Dave Stout's lab that involve allosteric fragments bound to these two sites on the surface of HIV protease are also being used as targets. Two of these new targets are presented in a new research manuscript from the Stout lab that is currently being peer-reviewed. When this paper is accepted, we will describe these targets in more detail and provide a link to this new paper.


This is by far the largest experiment we have submitted to FightAIDS@Home; it involves faah33,529 - faah45,253.

The results of these calculations started arriving at TSRI on 5/15/2012.
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 36,852

Days Left - 529

End Date - May 15, 2014

также, видео от ученых проекта

Webcast and Question & Answer session replay - featuring Lead World Community Grid Scientist Viktors Berstis and Dr. Alex Perryman:

http://www.worldcommunitygrid.org/about_us...o?articleId=213



This webcast commemorated World AIDS Day 2012 and gave World Community Grid members an opportunity to hear about the cutting-edge research being done with the FightAIDS@Home project. During the webcast, Dr. Perryman outlined the exciting discoveries that he and other members of Dr. Art Olson’s computational research lab have recently made in collaboration with other research teams at Scripps and around the world. They have run simulations that identified several chemical compounds that can “dock” with allosteric sites on the HIV protease molecule and may help to inhibit its function. These compounds could form the basis of therapeutic drugs to combat HIV “superbug” strains, and at the very least they suggest compelling new avenues for further research.

And the FightAIDS@Home research will continue, thanks to the World Community Grid volunteers. The computing power supplied by the members is absolutely critical to support this research and enable these advances in HIV treatment.

As always, thank you for your support of World Community Grid research projects and please stay tuned for future webcasts!
koc.gif
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 36,970

Days Left - 510

End Date - May 3, 2014
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,095

Days Left - 497

End Date - April 27, 2014
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,223

Days Left - 477

End Date - April 14, 2014
Rilian
December 30, 2012 update

WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,351

Days Left - 457

End Date - April 1, 2014

Project Completion - 32.61 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,483

Days Left - 443

End Date - March 25, 2014

Project Completion - 33.73 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,613

Days Left - 429

End Date - March 18, 2014

Experiment 41 Completion - 34.84 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,750

Days Left - 416

End Date - March 12, 2014

Experiment 41 Completion - 36.01 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,879

Days Left - 402

End Date - March 5, 2014
koc.gif
Experiment Completion - 37.11 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 37,998

Days Left - 395

End Date - March 5, 2014

Experiment Completion - 38.12 %
Rilian
Hi Everybody,

I just posted Volume 11 of the FightAIDS@Home Newsletter to:

IPB Image

http://fightaidsathome.scripps.edu/

FAAHvol11.pdf link.gif

This volume contains some of the same material that I presented in the last World AIDS Day Webinar , but I included more details and background information in the Newsletter.



Thank you all very much for your interest and your continued support,
Alex L. Perryman, Ph.D.
koc.gif
Rilian
QUOTE
Although I have processed and measured the results for Experiments 31 to 40, I have not yet had a chance to filter them and visually inspect the top-ranked compounds. After discovering these promising hits in Experiment 30, I've been focusing on hit-to-lead development (that is, trying to use the structures of these hits to guide the process of making larger, more potent compounds). I've also been spending a lot of time on the GO Fight Against Malaria project: preparing targets, performing and analyzing positive control studies, submitting experiments, and processing their results. I've also visually inspected and ordered new candidate compounds against two different classes of targets from the GO Fight Against Malaria project: PfSUB1 and InhA from Mycobacterium tuberculosis (which is very similar to ENR from malaria). I only need to prepare a few more classes of targets against malaria, and then I'll have more time to devote to analyzing the results of the other FightAIDS@Home experiments.

I will visually inspect and order compounds from FightAIDS@Home experiments 31 to 40, but it will take time.


Thank you very much for your interest and your support,
Alex L. Perryman, Ph.D.

link.gif


QUOTE
Hi branjo,

Thank you very much!

I just wish the faculty search committees appreciated my unconventional, ambitious strategies half as much as you all. In the past couple years, I've applied for around 150 different Assistant Professor positions at universities throughout the U.S. (and a few in Canada and Europe, and one in Taiwan). But I've had no luck yet. If I can get a faculty position, then I'll be able to seamlessly continue and extend this research for many more years, and I'll be able to bring more personnel and other resources on board, as well. Please wish me luck on this front, too. wink.gif It's still a tough job market for almost everyone, and that includes me.

Best wishes,
Alex L. Perryman, Ph.D.


Rilian
В 2012 году в Украине от СПИДа умерли почти четыре тысячи человек
Rilian
9-недельный Онлайн Курс по изучению СПИДа

https://www.coursera.org/course/aids
Rilian
20 или 21 февраля 2013 на 10 часов приостановится выдача заданий проекта всвязи с обновлением версии AutoDock

QUOTE
Temporary stoppage of the FAAH project (February 20th or 21st)
In order to switch FAAH to the new version of the science application (AutoDock), the FAAH project will temporarily be stopped. Since the switch needs to occur at a particular batch number, the exact time the outage will start can only be estimated. The current estimate is that the outage will happen on February 20th or 21st (this estimate will continue to be updated as the date approaches). The length of the outage is estimated to be less than 10 hours.

Seippel
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,150

Days Left - 429

End Date - April 22, 2014

Experiment Completion - 39.42 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,260

Days Left - 431

End Date - April 1, 2014

Experiment Completion - 40.36 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,362

Days Left - 439

End Date - April 16, 2014

Experiment Completion - 41.23 %
Rilian
Ученые в США сообщают, что им, судя по всему, удалось вылечить маленькую девочку, рожденную с вирусом ВИЧ,

http://korrespondent.net/tech/health/1515840 koc.gif
mysterix
опачки, нежданчик!
Brodyaga
QUOTE(Rilian @ Mar 4 2013, 09:07) *

Ученые в США сообщают, что им, судя по всему, удалось вылечить маленькую девочку, рожденную с вирусом ВИЧ,

http://korrespondent.net/tech/health/1515840 koc.gif

Хорошо бы. Правда непонятно почему стандартная программа лечения помогла только ей, я так понимаю что тот же курс назначают всем.
Bel
СКИФы против СПИДа
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,440

Days Left - 461

End Date - June 14, 2014

Experiment Completion - 41.90 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,571

Days Left - 456

End Date - June 16, 2014

Experiment Completion - 43.02%
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,713

Days Left - 439

End Date - June 6, 2014

Experiment Completion - 44.23 %

*** Above update is based on information from 3/24/2013 ***
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,844

Days Left - 424

End Date - May 29, 2014

Experiment Completion - 45.35 %
Rilian
Украина - один из лидеров по количеству больных ВИЧ-СПИД в Европе, но большинство людей с ВИЧ не имеет доступа к лекарственным препаратам, которые позволили бы им вести нормальную жизнь.

http://korrespondent.net/tech/health/1541071 koc.gif koc.gif koc.gif
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 38,912

Projected Days Left - 358

Projected End Date - March 22, 2014

Experiment Completion - 45.93 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 39,103

Projected Days Left - 327

Projected End Date - Feb 19, 2014

Experiment Completion - 47.55 %
Rilian
April 28, 2013 update
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 39,421

Projected Days Left - 284

Projected End Date - Feb 5, 2014

Experiment Completion - 50.27 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 39,602

Projected Days Left - 272

Projected End Date - February 1, 2014

Experiment Completion - 51.81 %
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 39,825

Projected Days Left - 242

Projected End Date - January 9, 2014

Experiment Completion - 53.72%
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 40,056

Projected Days Left - 217

Projected End Date - December 22, 2013

Experiment Completion - 55.69%
Rilian
я почитал внимательнее описание текущего эксперимента номер 41 -- http://fightaidsathome.scripps.edu/status

QUOTE
Experiment 41 involves screening the Enamine library of 2.345 million compounds against the two allosteric sites on the surface of HIV protease. This experiment is similar to Exp. 36, but a different, much larger library of compounds is being screened, and some new targets are being included. The first part of this experiment involves docking compounds against the two allosteric-fragment-bound crystal structures presented in our recent article in Chemical Biology and Drug Design, vol. 75: 257-268 (March 2010). Three other, brand new crystal structures from Dave Stout's lab that involve allosteric fragments bound to these two sites on the surface of HIV protease are also being used as targets. Two of these new targets are presented in a new research manuscript from the Stout lab that is currently being peer-reviewed. When this paper is accepted, we will describe these targets in more detail and provide a link to this new paper.


Alien может меня поправить, но как я понял, Alex Perryman, главный ученый FAAH и GFAM, открыл новый способ рассчитывать ингибиторы к белкам, используя только опеределенную часть белка. То есть с помощью рентгеновской кристаллографии они определяют 3Д структуру части белка, оцифровывают ее, и используют докинг, перебирая все возможные синтетические белки, чтобы проверить их влияние на исходный белок, участвующий в образовании определенных болезней (ВИЧ, малярия).

В тексте также пишется что помимо 2 своих частей белков ВИЧ, Алекс использует 3 новых структуры из лаборатории Dave Stout -- http://www.scripps.edu/stout/Stout%20Websi...blications.html

Я зашел на их сайт, и у этой лаборатории за 5 месяцев этого года (2013) уже сделано 9 публикаций!

Вобщем, можно сказать что FAAH находится на самом передовом фронте биоинформатических исследований, и очень важно их поддерживать в данный момент! koc.gif
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 40,247

Projected Days Left - 200

Projected End Date - December 12, 2013

Experiment Completion - 57.32%
Alien
QUOTE(Rilian @ May 25 2013, 10:53) *

Alien может меня поправить, но как я понял, Alex Perryman, главный ученый FAAH и GFAM, открыл новый способ рассчитывать ингибиторы к белкам, используя только опеределенную часть белка. То есть с помощью рентгеновской кристаллографии они определяют 3Д структуру части белка, оцифровывают ее, и используют докинг, перебирая все возможные синтетические белки, чтобы проверить их влияние на исходный белок, участвующий в образовании определенных болезней (ВИЧ, малярия).

Я не вчитывался, но там идея должна быть такой.
Получаем координаты белка, а если его какой-то части нет - домоделировать.
Далее оптимизировать структуру, а потом если известен активный сайт подбирать к нему лиганды.
Судя по всему, они ищут несколько сайтов на белке, что интересно.
Вижу в его статье 2011 года они используют МД, что есть правильно, т.к. структура полученная после кристаллизации не есть конформационно нативной, в отличии от полученной методом ЯМР.

То есть, результаты полученные после докинга на часть кристалла не есть информативными и являются малоперспективными без дальнейшего изучения комплекса методам МД. Они могут иметь малую корреляцию с экспериментом, а успешность подбора может и не достигать 0.1 %.
Подобранный успешный лиганд может еще негативно влиять на один из остальных 99.99% белков из-за чего он не будет внедрен в практику лечения.

Вывод: необходимо обращать внимание на работы, которые используют современные подходы к изучению проблемы. Это комбинированные методы докинг->МД->ММ\КМ. Докинг на статическую структуру да и еще рентген мало что даст на практике.

У нас тоже проводили изучения на вич протеазе - http://librar.org.ua/sections_load.php?s=b...sciences&id=303 (можно скачать автореферат).
Rilian
Спасибо. Значит все хорошо!

Алиен, просьба, пройдись по всем активным проектам и выскажи свое мнение как ученого об их методах вычислений и пользе науке!
Alien
постараюсь в четверг\пятницу проглянуть.
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 40,250

Projected Days Left - 187

Projected End Date - December 1, 2013

Experiment Completion - 57.34%

Projected WU remaining approximately 23,000,000

Cheers
Rilian
http://www.3dnews.ru/news/646022 koc.gif
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 40,665

Projected Days Left - 156

Projected End Date - November 11, 2013

Experiment Completion - 60.88%
Rilian
Новая информация о проекте

We also started collaborating with many other prominent experts on HIV, as part of a newly-created Center called the "HIVE". See: http://fightaidsathome.scripps.edu/ and http://hive.scripps.edu/ . In fact, we will soon expand the FightAIDS@Home project and start targeting three different allosteric sites on HIV reverse transcriptase that were recently discovered and three different allosteric sites of HIV integrase that were also recently discovered. In addition, we will soon add the ability to perform docking calculations with the software "AutoDock Vina" on FightAIDS@Home, which will enable us to increase the speed and scale of our virtual screens against these three drug targets from HIV/AIDS by several orders of magnitude.

Вкратце, создан новый центр по изучению ВИЧ

А также, проект будет проводить эксперименты на 6 недавно открытых точках ВИЧ
excl.gif

IPB Image

Мы на самом остром краю исследований! koc.gif koc.gif koc.gif

link.gif
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 41041

Projected Days Left - 128

Projected End Date - October 22, 2013

Experiment Completion - 64.09%

Projected WU remaining approximately 19,300,000
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 41504

Projected Days Left - 99

Projected End Date - September 29, 2013

Experiment Completion - 68.04%

осталось ВЮ із єксперімента 41: 17,150,000
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 41994

Projected Days Left - 76

Projected End Date - September 13, 2013

Experiment Completion - 72.22%

Projected WU remaining approximately 14,892,000

At the present rate we are chewing through about 4% of the experiment 41 per week.
Rilian
WEEKLY UPDATE - based on work averaged over the last 8 weeks:

Current Batch - 42428

Projected Days Left - 61

Projected End Date - September 06, 2013

Experiment Completion - 75.92%

Projected WU remaining approximately 12,947,000

The pace is still accelerating with over 2,000,000 WU in the last seven days.


--

Интересно, какой будет новый эксперимент?
Rilian
график завершения эксперимента 41

IPB Image

когда синяя линия пересечется с зеленой, эксперимент завершен smile.gif
.
Invision Power Board © 2001-2022 Invision Power Services, Inc.