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Rilian
Aug 31 2011, 21:51
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Проект "Drug Search for Leishmaniasis"

Проект запущен 31 Августа 2011

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Как присоединиться читайте в главном топике World Community Grid thumbsup.gif



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Дата основания команды - 28.02.2005 Капитан - rilian
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О проекте:

Mission
The mission of Drug Search for Leishmaniasis is to identify potential molecule candidates that could possibly be developed into treatments for Leishmaniasis. The extensive computing power of World Community Grid will be used to perform computer simulations of the interactions between millions of chemical compounds and certain target proteins. This will help find the most promising compounds that may lead to effective treatments for the disease.

Significance
Leishmaniasis is one of the most neglected tropical diseases in the world. Each year this disease infects more than two million people in 97 countries. To date, there are no available vaccines to prevent the disease, in spite of multiple research efforts. Leishmaniasis is caused by a protozoan parasite (genus Leishmania) transmitted between human and animal hosts by female sand flies. One form of the disease, the "visceral" form caused by Leishmania infantum in America, mainly affects children, who can die if adequate treatment is not provided promptly. Existing control measures rely upon drug therapy, insect control and education in the affected communities. However, the number of human cases continues to increase in tropical countries such as Bangladesh, India, Sudan, Ethiopia, Brazil, Colombia, Peru and many others.

The classical treatments for all forms of Leishmaniasis can cause severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe and inexpensive anti-Leishmania drug compounds.

Approach
A software program called VINA from The Scripps Research Institute in La Jolla, California, will be used to perform the virtual chemistry experiments. These virtual experiments will search to find which of millions of drug compounds might be able to disable particular proteins, essential for the parasite's survival. Screening for the best potential drug compounds is an early step in the process of developing effective treatments for the disease. With enough computing power, this screening can be done much more quickly than using conventional laboratory experiments. However, existing computer facilities available to the researchers would require approximately 120 years to perform the screening. The power of World Community Grid can reduce the time required to less than one year. Information about the best candidate compounds will be published by the scientists, and this information will be available in the public domain for other scientists to build upon with their research. Further laboratory work using the best candidates identified by this project could lead to the development of better drugs to fight Leishmaniasis.

About the Project

Leishmaniasis is a tropical disease caused by a parasite transmitted by specific insects. Infections of this disease have been increasing - with over two million people affected last year. Existing treatments can have severe side effects, including death. Currently, pharmaceutical companies have not been investing in extensive research to combat this disease. Therefore, the researchers at the University of Antioquia in Medellín, Colombia, are running a project on World Community Grid to search for chemical compounds which may lead to new drugs for treating this disease.

Leishmaniasis is caused by a single celled protozoan parasite. The genus of this protozoan is Leishmania. It is transmitted between human and animal hosts via the female sand fly. In the Americas, the genus of the sand fly is Lutzomyia and elsewhere it is Phlebotomus. The insect injects humans or other animals with promastigotes, the infective stage of the parasite. Once injected into the skin, the promastigote infects immune system cells such as macrophages and other mononuclear phagocytic cells. Within these cells, the promastigote transforms into the tissue stage of the parasite, known as amastigote, which multiplies inside the cell by simple division, moving on to infect other phagocytic mononuclear cells. Various factors of the parasite and host determine which form of the diseases appears in the host. The insects become infected by sucking infected cells of the host during a blood meal. In the insect´s gut, the cells rupture releasing amastigotes, which are transformed back into promastigotes. They multiply and develop in the insect's gut. After several days, depending on the species, the parasites migrate to the mouthparts of the insect, where they are ready again to be transmitted to a host, during the next blood meal.

The disease has three clinical forms:
* cutaneous - affecting the surface skin consisting mostly of ulcerated lesions, warty lesions or spots.
* mucocutaneous - affecting mucous membranes, particularly from the nose, laryngeal and pharynx.
* visceral - affecting bone marrow or internal organs, such as the liver, spleen and lymph nodes. Symptoms can include anemia, clotting problems, weight loss, enlarging of the spleen, liver and lymph nodes.

The classical treatments for all forms of Leishmaniasis are certain compounds of pentavalent antimony (e.g. sodium stibogluconate and meglumine antimoniate). These compounds can have severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. Several additional drugs such as Pentamidine and Amphotericin B have been used with variable success, but these drugs also have serious side effects and are expensive and difficult to administer, limiting their use as drugs of choice. More recently, Miltefosine (an oral drug) has been used with variable success in Central and South America against cutaneous Leishmaniasis and for visceral Leishmaniasis in India. A phase IV trial of this drug in India has shown an increase in the relapse rate, indicating that drug resistance may develop quickly. The visceral form mainly affects children, who can die if adequate treatment is not provided promptly.

The complete genomes of several Leishmania species have been decoded and are providing information about proteins and processes essential for the survival of the parasite. Certain Leishmania proteins have been identified as targets using information about the genomes and through prior laboratory experiments and computational work. If drugs can be developed to disable these proteins, they may prove to be an effective treatment for the disease. The first step in drug development is to find chemical compounds which attach to the target protein in a manner that disables the protein's function, thus preventing the progression of the disease. To accelerate the search for potential drugs against Leishmaniasis, the computing power of World Community Grid will be used to screen millions of potential chemical compounds as possible drug treatment candidates. Instead of performing expensive and time-consuming laboratory experiments, simulations of these millions of experiments will be performed using the software running on World Community Grid's member computers.

A software program called VINA from The Scripps Research Institute in La Jolla, California, will be used to perform the virtual chemistry experiments, more precisely known as molecular dockings. Molecular docking is the process of determining how well two chemical compounds (molecules) bind together. One of the molecules is designated as the target, in this case one of several proteins, essential for the parasite's survival. The other compound is from a collection of millions of compounds from various drug data bases, cataloging known compounds and their exact atomic structure. The docking experiments position the two compounds in all possible orientations and then compute the binding energy, which tells how well they stick together. If a compound binds to the target protein, it may be useful in disabling the function of that protein and thus reducing parasite multiplication and the progress of the disease.

The VINA calculations will be used to identify the most promising chemical compounds that may inhibit these proteins. The computer computations involved are very intensive and would take about 120 years to test the 12 million compounds against 70 Leishmania proteins, if using machines normally available to the researchers. World Community Grid will be able to reduce the time required to less than one year. Information about the best candidate compounds will be published by the scientists, and this information will be available in the public domain for other scientists to build upon with their research. Further laboratory work using the best candidates identified by the VINA computations could lead to the development of better drugs to fight Leishmaniasis.

Наименования рабочих заданий и их количество (обновлено 31 августа 2011)

Work unit numbering is in this format:
DSFL_TTTTTTTT_BBBBBBB_WWWW
T=Target
B=Batch
W=Work unit number

Сейчас кол-во целей (target) 5353, и в каждой 58 пачек (batch). В каждой пачке примерно 1000 заданий, с кворумом 2
Учитывая что время задания в среднем 6 часов, получаем 5353*58*1000*2*6= 3,725,688,000 часов = 425000 процессорных лет orly.gif censoree.gif
Добавляя 6% на разные ошибки и таймауты, получается ~450000 процессорных лет, или 450000/345 = 1300 WCG дней (если бы считался только этот проект) suicide.gif

Команда

Stan Watowich, The University of Texas Medical Branch (Galveston, Texas, USA) -- помошник, координатор DDDT2
Carlos Muskus, PECET, University of Antioquia, Medellín, Colombia
Andres Florez, PECET, University of Antioquia, Medellín, Colombia
Rodrigo Ochoa, PECET, University of Antioquia, Medellín, Colombia

Ссылки по теме:Как происходят рассчеты: программа подбирает структуру поглощающей поверхности и подвергает ее воздействию освещения. Поверхность выделяет электроэнергию и нагревается. Программа измеряет эти параметры со временем

Видео о проекте (скачать link.gif )


Как выглядит графический клиент:


График работы проекта


Це повідомлення відредагував nikelong: Mar 17 2012, 22:34
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Rilian
Sep 7 2011, 18:22
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Розсилка про проект!

http://www.worldcommunitygrid.org/about_us...o?articleId=170

Launch of the Drug Search for Leishmaniasis Project

Category: Drug Search for Leishmaniasis
Tags: Accomplishments , Project Update , Project Event

Summary
World Community Grid is pleased to announce the launch of the Drug Search for Leishmaniasis project.

This project is provided by the University of Antioquia in Medellín, Colombia, with assistance from researchers at the University of Texas Medical Branch in Galveston, Texas. This project hopes to identify potential molecule candidates that could possibly be developed into treatments for Leishmaniasis

Leishmaniasis is one of the most neglected tropical diseases in the world. Each year this disease infects more than two million people in 97 countries. To date, there are no available vaccines to prevent the disease.

Existing control measures rely upon drug therapy, insect control and education in the affected communities. However, the number of human cases continues to increase in tropical countries such as Bangladesh, India, Sudan, Ethiopia, Brazil, Colombia, Peru and many others.

The classical treatments for all forms of Leishmaniasis can cause severe side effects, and even lead to death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe and inexpensive anti-Leishmania drug compounds.

A software program called VINA from The Scripps Research Institute in La Jolla, California, will be used to perform the virtual chemistry experiments. These virtual experiments will search to find which of millions of drug compounds might be able to disable particular proteins, essential for the parasite's survival. Screening for the best potential drug compounds is an early step in the process of developing effective treatments for the disease. With enough computing power, this screening can be done much more quickly than using conventional laboratory experiments.

For additional information on this project, please press the Research button in the upper navigation bar or click here.

Participation in the Drug Search for Leishmaniasis project

Drug Search for Leishmaniasis is the eighteenth research project to be launched on World Community Grid and one of nine projects currently running on World Community Grid. The other eight research projects are:
Computing for Clean Water (launched August, 2010)
The Clean Energy Project – Phase 2 (launched June, 2010)
Discover Dengue Drugs – Together – Phase 2 (launched February, 2010)
Help Cure Muscular Dystrophy – Phase 2 (launched May, 2009)
Help Fight Childhood Cancer (launched March, 2009)
Help Conquer Cancer (launched November, 2007)
Human Proteome Folding - Phase 2 (launched July, 2006)
FightAIDS@Home Phase 2 (launched November, 2005)

For more detailed information and FAQs about each of these projects, please click on the Research button in the upper navigation bar. We thank all of our members for their valuable contributions to the projects to date and hope you will continue to help us process those, as well as this latest project.

Because there are nine research projects running on World Community Grid, your grid agent could receive work units from any of the projects depending on your Project profile. If you prefer, you may elect to focus your computer's time only on particular projects. To do so, press the My Grid button in the upper navigation bar and select My Projects or click here. Work is sent only to machines which meet minimum system requirements set for a particular project. To read more specifics on the system requirements for the Drug Search for Leishmaniasis project and the other projects, click here.

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If a member contributes a minimum of 14 days of CPU Run Time to this project, they will receive a Drug Search for Leishmaniasis project badge on their member statistics page and next to their member name when they post in the forums. There is a different badge for each research project and beta testing. To read more about badges, click here.

Forums

In addition to providing information about this project, we have created a forum for discussions about the Drug Search for Leishmaniasis project. To participate in this forum, please press the Forums button in the upper navigation bar or click here. Only forum authors with the title "Drug Search for Leishmaniasis Scientist" are authorized to comment as representatives of the University of Antioquia in Medellín, Colombia.

Questions?

If you have any questions, World Community Grid provides you with four methods of obtaining assistance: (1) Review the FAQs found in the Help section of the website; (2) Review the forums to see if anyone has asked/answered the question that you have; (3) Ask the question in World Community Grid's Drug Search for Leishmaniasis project forum found here and a Community Advisor or a more experienced member will provide an answer; or (4) Send an email to the support desk from the Contact Us link found at the bottom of every page of the website (except in the forums).

We thank you for contributing to the Drug Search for Leishmaniasis project. bq.gif

Всім приємних розрахунків на користь людства!


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tiss
Sep 7 2011, 18:29
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(Rilian @ Sep 7 2011, 19:22) *

Розсилка про проект!


А у меня уже золотой беджик smile.gif


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Rilian
Sep 8 2011, 10:21
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Leishmaniasis is one of the most neglected tropical diseases. Each year it infects more than two million people in 97 countries. To date, there are no available vaccines to prevent the disease. Researchers at the University of Antioquia in Medellin, Colombia, are running the Drug Search for Leishmaniasis project on World Community Grid to identify drug compounds that could possibly be developed into treatments for Leishmaniasis.


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Salmonella
Sep 9 2011, 05:25
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Что-то все вдруг вспомнили про "забытые" болезни. Модный тренд не иначе. smile.gif Полез к Д. Бейкеру на сайт, и у них там в разделе "Structure-Based Drug Design". Внезапно: smile.gif
Larson E.T., Kim J.E., Castaneda L.J., Napuli A.J., Zhang Z., Fan E., Zucker F.H., Verlinde C.L.M.J., Buckner F.S., Van Voorhis W.C., Hol W.G.J., Merrit E.A. (2011). Tyrosyl tRNA-synthetase from the eukaryote Leishmania major is monomeric but forms an intrinsically asymmetric pseudo-dimer. J. Mol. Biol. 409: 159-176. [PMID: 21420975]
Shibata S., Gillespie J.R., Kelley A.M., Napuli A.J., Zhang Z., Kovzun K.V., Pefley R.M., Lam J., Zucker F., Van Voorhis W.C., Merritt E.A., Hol W.G.J., Verlinde C.L.M.J., Fan E., Buckner F.S. (2011). Selective inhibitors of methionyl-tRNA synthetase have potent activity on Trypanosoma brucei infection in mice. Antimicrob. Agents Chemother. 55: 1982-1989. [PMID: 21282428]
Merritt E.A., Arakaki T.L., Gillespie R., Napuli A.J., Kim J.E., Buckner F.S., Van Voorhis W.C., Verlinde C.L.M.J., Fan E., Zucker F., Hol W.G.J. (2011). Crystal structures of three protozoan homologs of tryptophanyl-tRNA synthetase. Mol. Biochem. Parasitol.177: 20-28. [PMID: 21255615]
Ojo K.K., Arakaki T.L., Napuli A.J., Kishore K., Keyloun K.R., Zhang L., Hol W.G.J., Verlinde C.L.M.J., Merritt E.A. Van Voorhis W.C. (2011). Structure Determination of Glycogen Synthase Kinase-3 from Leishmania major Explains a Distinct Inhibitor Structure Activity Relationship Compared with Trypanosoma brucei GSK-3. Mol. Biochem. Parasitol.176: 98-108. [PMID: 21195115]
Larson E.T., Kim J.E., Zucker F., Kelley A., Mueller N., Napuli A.J., Verlinde C.L.M.J., Fan E., Buckner F.S., Van Voorhis W.C., Merritt E.A., Hol W.G.J. (2011). Structure of Leishmania major methionyl-tRNA synthetase in complex with intermediate products methionyladenylate and pyrophosphate. Biochimie 93: 570-582. [PMID: 21144880]
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Rilian
Sep 9 2011, 10:41
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Salmonella, дай посилання. не знайшов на сайті Розетти


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Sep 9 2011, 12:17
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Это на факультете у Бейкера на сайте Университета. Тыкал ссылки. smile.gif А Бейкера приплёл потому что он Гуру. smile.gif Забавно, получилось, практически все статьи по Лейшманиозу за 2011 год, за другие года - почти ничего. Случайность если хотите. smile.gif
Вашингтонский универ тоже протозойными болезнями занимается.
http://www.sgpp.org/members.shtml
http://www.msgpp.org/members.shtml
http://depts.washington.edu/bmsd/people/faculty.php
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Rilian
Sep 30 2011, 15:33
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Sep 30 2011, 15:43
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Мне вот бронза капнула - мелочь, а приятно shuffle.gif koc.gif
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Sep 30 2011, 17:47
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мрію про ферму...
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Уже вернулся отсюда на НСС, там очков меньше, но вроде нужнее.


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Sep 30 2011, 17:50
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QUOTE(london2004 @ Sep 30 2011, 18:47) *

Уже вернулся отсюда на НСС, там очков меньше, но вроде нужнее.

Там проект через 20 дней закончится. Устроим финишный спурт?


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Rilian
Sep 30 2011, 18:06
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QUOTE(london2004 @ Sep 30 2011, 18:47) *

Уже вернулся отсюда на НСС, там очков меньше, но вроде нужнее.

мне тут подкинули 16-ядерную машину (по 2 ггц) - на ней быстро бейджики зарабатываются - по 20 дней в день. Потом сразу обратно на ХЦЦ


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Rilian
Oct 11 2011, 10:26
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пока я переключился на HCC + HFCC для соревнования, у меня навалидировалось ВЮх на изумруд (1 год)

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Вернусь сюда в ноябре, добить еще 1 год для сапфира



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Rilian
Apr 16 2012, 17:28
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04 Apr 2012

The scientists working on the Drug Search for Leishmaniasis project on World Community Grid have written a chapter in the book "Current Topics in Tropical Medicine".

A link to this open science book can be found here: Current Topics in Tropical Medicine. link.gif

Chapter 16, entitled "Current Advances in Computational Strategies for Drug Discovery in Leishmaniasis", describes the scientific details of identifying drug targets and drug candidates and mentions how World Community Grid plays a role in the process. You may read the text of this chapter here.


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Apr 16 2012, 18:00
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Rilian
Jun 6 2012, 14:49
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