FightAIDS@home, поиск лекарств от ВИЧ и СПИДа Налаштування

[Rilian]

Проект занимается подбором лекарств от ВИЧ

* Официальный сайт
* Прогресс и статус исследований на официальном сайте

Как присоединиться читайте в главном топике World Community Grid

Подробнее о научных методах в FightAIDS@Home:

Белки, как вы уже знаете, является строительным материалом для всех живых существ. Разнообразные формы белков принимают участие во всех процессах, происходящих в живых организмах. Белки являются длинными цепями меньших молекул - аминокислот.

Энзимы являются конкретными типами белков, которые ускоряют биохимические реакции.

Протеаза - энзим, который способен «вырезать» отдельный белок в некоторой точке аминокислотной цепи. Например, когда Вы едите пищу, которая также содержит белок, белковые молекулы режутся на меньшие аминокислотные молекулы протеазой в вашем желудке.

Ваш организм может затем использовать получившиеся аминокислоты, чтобы формировать белки, которые ему нужны для продолжения жизнедеятельности. Стоит отметить также, что только небольшой процент из всех белков в организме является протеазами, поэтому эти белки очень важны в своем функционировании для обеспечения жизненных процессов.

Ваш компьютер поможет нам имитировать процесс присоединения множества различных лиганд* к HIV-протеазе (HIV- Human Immunodeficiency Virus – вирус иммунодефицита человека), для этого используется компьютерная программы под названием AutoDock.

*Лиганды - (от лат . ligo - связываю), в комплексных соединениях молекулы или ионы, связанные с центральным атомом (комплексообразователем), напр. в соединении [Co(NH3)6]Cl3 центральный атом - Со, а лиганды - молекулы NH3.

Перспективные лиганды будут изучены более подробно учеными, и это должно привести нас к созданию лекарства для управления ВИЧ-инфекцией, и в конце концов, к предотвращению заболевания СПИДОМ.

Естественно, моделирование таких процессов – сложная в вычислительном отношении задача из-за большого разнообразия белковых структур и выделению из них тех, которые могут эффективно повлиять на вирус, поэтому в данном проекте также используются методы распределенных вычислений.

What is AIDS?
UNAIDS, the Joint United Nations Program on HIV/AIDS, estimated that in 2004 there were more than 40 million people around the world living with HIV, the Human Immunodeficiency Virus. The virus has affected the lives of men, women and children all over the world. Currently, there is no cure in sight, only treatment with a variety of drugs.

Prof. Arthur J. Olson's laboratory at The Scripps Research Institute (TSRI) is studying computational ways to design new anti-HIV drugs based on molecular structure. It has been demonstrated repeatedly that the function of a molecule — a substance made up of many atoms — is related to its three-dimensional shape. Olson's target is HIV protease ("pro-tee-ace"), a key molecular machine of the virus that when blocked stops the virus from maturing. These blockers, known as "protease inhibitors", are thus a way of avoiding the onset of AIDS and prolonging life. The Olson Laboratory is using computational methods to identify new candidate drugs that have the right shape and chemical characteristics to block HIV protease. This general approach is called "Structure-Based Drug Design", and according to the National Institutes of Health's National Institute of General Medical Sciences, it has already had a dramatic effect on the lives of people living with AIDS.

Even more challenging, HIV is a "sloppy copier," so it is constantly evolving new variants, some of which are resistant to current drugs. It is therefore vital that scientists continue their search for new and better drugs to combat this moving target.

Scientists are able to determine by experiment the shapes of a protein and of a drug separately, but not always for the two together. If scientists knew how a drug molecule fit inside the active site of its target protein, chemists could see how they could design even better drugs that would be more potent than existing drugs.

To address these challenges, World Community Grid's FightAIDS@Home project runs a software program called AutoDock developed in Prof. Olson's laboratory. AutoDock is a suite of tools that predicts how small molecules, such as drug candidates, might bind or "dock" to a receptor of known 3D structure. The very first version of AutoDock was written in the Olson Laboratory in 1990 by Dr. David S. Goodsell, since then, newer versions, developed by Dr. Garrett M. Morris, have been released which add new scientific understanding and strategies to AutoDock, making it computationally more robust, faster, and easier for other scientists to use. From the beginning of this project, World Community Grid has been running a pre-release version of AutoDock4. In August 2007, World Community Grid started running the new publicly available version 4 of AutoDock which is faster, more accurate, can handle flexible target molecules and thus can also be used for protein-protein docking analysis. AutoDock is used in the FightAIDS@Home project on World Community Grid to dock large numbers of different small molecules to HIV protease, so the best molecules can be found computationally, selected and tested in the laboratory for efficacy against the HIV virus. By joining forces together, The Scripps Research Institute, World Community Grid and its growing volunteer force can find better treatments much faster than ever before.

График проекта


Ссылки

ВИЧ 3D

Це повідомлення відредагував Rilian: Sep 8 2010, 11:49

[mysterix]

конечно)

[Death]

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!

[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

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:



http://fightaidsathome.scripps.edu/

FAAHvol11.pdf

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.

[Rilian]

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.

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. It's still a tough job market for almost everyone, and that includes me.

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