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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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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
Jul 12 2012, 11:02
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Thanks for all people supporting the DSFL project

Dear WCG members.

This is a short message just to thanks all members (crunchers) of the WCG supporting the project Drug Search for Leishmaniasis (DSFL) for the almost 19 millions results processed and returned to the World community grid out of the 1 billion results results. Hope we can continue receiving this help to try to get a new safe and cheap drug for the leishmaniasis treatment.

Best wishes from Colombia and thanks again


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Jul 12 2012, 11:46
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19 millions results processed and returned to the World community grid out of the 1 billion results results

то есть 1.9% посчитали?


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Rilian
Jul 12 2012, 11:48
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QUOTE(Death @ Jul 12 2012, 12:46) *

19 millions results processed and returned to the World community grid out of the 1 billion results results

то есть 1.9% посчитали?

нет, просто недавно ВЦГ преодолели рубеж в 1 МЛРД посчитанных заданий, из них 1.9% это ДСФЛ


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Rilian
Jul 26 2012, 10:37
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Апдейт проекта

Drug Search for Leishmaniasis Update

Rodrigo Ochoa and Carlos Muskus

The project “Drug Search for Leishmaniasis” has been running during 10 months, and the following is a brief description of our progress and what have been validated until now:

The original project included the evaluation of 53 crystallized Leishmania proteins obtained from the PDB database along with 5,300 modelled structures, (100 modelled structures for each protein downloaded from PDB) (figure 1). The modelling was carried out through Molecular Dynamics using the NAMD program, representing an indirect way to provide flexibility for each one of the potential targets.

However, based on the statistic of the project after 6 months of activity, to run the 5.353 protein structures against the 600.000 compounds will spend around 20-25 years to complete. These made us to reconsider the project just prioritizing 10 structures for each of the 53 proteins for a total of 530 structures (Phase 2). Originally the idea was to build a molecular trajectory using snapshots of a protein during a computational simulation, trying to mimic the biological environment of the protein inside the organism. The trajectories contain 100 snapshots. Nevertheless, to prioritize the data, 10 snapshots per trajectory (i.e from the 100 structures per protein, the snapshots 10, 20, 30, 40, 50, 60, 70, 80 90 and 100 were selected) (see figure 2). That rational selection pretends to cover substantial changes in the conformation of the binding site of the protein.

Currently, WCG have processed approx. 76.200.000 docking simulations (127 structures against 600.000 compounds in phase I). From the second phase, it has processed approx. 37.800.000 docking simulations (63 priority structures against the same 600.000 compounds). Due to the huge amount of data, only the top 20 compounds per structure (compounds with the best score hits) and based on the score function proposed by the AutoDock VINA software, have been extracted. As an example, we provided the top 20 compound which lists from the protein 1-10, 1-20 and 1-30* (See tables 1, 2 and 3)
*The notation 1-10 means the modelled structure 10, from the protein target 1 of the 53 original proteins downloaded from PDB database.
A future analysis with the high relevant results will be published in the next update of the project.

IPB Image
Figure 1. Representation of the 53 original PDB proteins (black-red squares at the bottom), and the 5300 (blue squares) modelled proteins. Solid Red squares along with the black-red squares represent 127 proteins that were already docked against the 600.000 compounds in the first phase of the project


IPB Image
Figure 2. Priority targets (530 structures) are represented by solid red squares and are being docked against the 600.000 compounds. Modelled protein 1 is more similar in structure to the original proteins obtained from PDB than modeled protein structure 100. Sixty three priority structures out of the 530 have been already docked against the 600.000 compounds.

Table 1. Top 20 docking results for modelled structure 10 from the protein target number 1.
IPB Image

Table 2. Top 20 docking results for modelled structure 20 from the protein target number 1.
IPB Image

Table 3. Top 20 docking results for modelled structure 30 from the protein target number 1.
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Aug 25 2012, 09:50
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Среднее время выполнения всех заданий увеличилось на 20%!
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Nov 1 2012, 12:11
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Current status of the Drug Search for Leishmaniasis project

When we initially launched the project in September 2011 on World Community Grid, we planned on using Autodock-Vina to evaluate the docking of 5,353 protein structures from the Leishmania parasite against 600,000 chemical compounds selected and filtered from the ZINC database. The software measures the protein-compound interaction in a three dimensional space and generates a score according to the degree of affinity. The 5,353 protein structures correspond to 53 Leishmania proteins for which the crystal structures were obtained from x-ray crystallography information found in the Protein Data Bank (PDB) along with 100 alternate modeled protein structures for each of the 53 original structures. However, the rate of progress showed that it would take 20-25 years to compute all of these interactions. Therefore we prioritized the 5,353 structures and focused on just 530 modeled structures along with the 53 original PDB structures for a total of 583 structures. This would give us useful results much sooner.

The table loaded in the news section at PECET website summarizes the status of the DSFL project. Each of the cells on the table corresponds to any of the 5,353 structures, both original and modeled. The green cells correspond to the 53 original structures from PDB (bottom horizontal row) and 75 modeled structures of the first PDB protein (first column) already docked before prioritizing the 530 structures. The blue cells correspond to the 530 modeled and prioritized structures that have been already docked against the 600,000 compounds. And finally, the red cells correspond to those 530 priority structures pending to be processed.

We give a very big “thank you” to the World Community Grid members for contributing to this project!

Кратко: всего надо ісследовать взаімодействіе 5353 белков, із ніх 530 рассчітиваются с большім пріорітетом так как оні важнее. В таблічке видно существующий прогресс IPB Image

http://www.worldcommunitygrid.org/forums/w...ad_thread,34157


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Feb 7 2013, 20:01
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Mar 26 2013, 14:38
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Апдейт проекта

посчитано 67%

Drug Search for Leishmaniasis Update

Rodrigo Ochoa and Carlos Muskus





The project “Drug Search for Leishmaniasis” has been running during 10 months, and the following is a brief description of our progress and what have been validated until now:

The original project included the evaluation of 53 crystallized Leishmania proteins obtained from the PDB database along with 5,300 modelled structures, (100 modelled structures for each protein downloaded from PDB) (figure 1). The modelling was carried out through Molecular Dynamics using the NAMD program, representing an indirect way to provide flexibility for each one of the potential targets.

However, based on the statistic of the project after 6 months of activity, to run the 5.353 protein structures against the 600.000 compounds will spend around 20-25 years to complete. These made us to reconsider the project just prioritizing 10 structures for each of the 53 proteins for a total of 530 structures (Phase 2). Originally the idea was to build a molecular trajectory using snapshots of a protein during a computational simulation, trying to mimic the biological environment of the protein inside the organism. The trajectories contain 100 snapshots. Nevertheless, to prioritize the data, 10 snapshots per trajectory (i.e from the 100 structures per protein, the snapshots 10, 20, 30, 40, 50, 60, 70, 80 90 and 100 were selected) (see figure 2). That rational selection pretends to cover substantial changes in the conformation of the binding site of the protein.

Currently, WCG have processed approx. 76.200.000 docking simulations (127 structures against 600.000 compounds in phase I). From the second phase, it has processed approx. 37.800.000 docking simulations (63 priority structures against the same 600.000 compounds). Due to the huge amount of data, only the top 20 compounds per structure (compounds with the best score hits) and based on the score function proposed by the AutoDock VINA software, have been extracted. As an example, we provided the top 20 compound which lists from the protein 1-10, 1-20 and 1-30* (See tables 1, 2 and 3)

*The notation 1-10 means the modelled structure 10, from the protein target 1 of the 53 original proteins downloaded from PDB database.

A future analysis with the high relevant results will be published in the next update of the project.

IPB Image

Figure 1. This new graph represent the current progress of the 583 priority targets (530 modelled proteins + 53 original structures) docked against the 600.000 compounds. The red bar at the botton of the figure represents the 53 original proteins structures already docked. The others bars represent the modelled protein structures (from 10 to 100). The blue color areas represent modelled proteins already docked and the green color areas represent the modelled proteins pendindg for docking. As you can see there are 203 modelled structures pending for docking which correspond to approximately 35%.

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Rilian
Apr 13 2013, 11:09
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DSFL update - April 11, 2013

QUOTE
Dear DSFL Collaborators

With your help or contribution, 71% of the priority proteins have been processed against the 600.000 compounds. According to the statistic of the project, it is estimated to end in the middle of august this year.

An update of the project have been loaded in the project website: link.gif

Thank to all of you for your collaborations.


The project “Drug Search for Leishmaniasis” has been running during 10 months, and the following is a brief description of our progress and what have been validated until now:

The original project included the evaluation of 53 crystallized Leishmania proteins obtained from the PDB database along with 5,300 modelled structures, (100 modelled structures for each protein downloaded from PDB) (figure 1). The modelling was carried out through Molecular Dynamics using the NAMD program, representing an indirect way to provide flexibility for each one of the potential targets.

However, based on the statistic of the project after 6 months of activity, to run the 5.353 protein structures against the 600.000 compounds will spend around 20-25 years to complete. These made us to reconsider the project just prioritizing 10 structures for each of the 53 proteins for a total of 530 structures (Phase 2). Originally the idea was to build a molecular trajectory using snapshots of a protein during a computational simulation, trying to mimic the biological environment of the protein inside the organism. The trajectories contain 100 snapshots. Nevertheless, to prioritize the data, 10 snapshots per trajectory (i.e from the 100 structures per protein, the snapshots 10, 20, 30, 40, 50, 60, 70, 80 90 and 100 were selected) (see figure 2). That rational selection pretends to cover substantial changes in the conformation of the binding site of the protein.

Currently, WCG have processed approx. 76.200.000 docking simulations (127 structures against 600.000 compounds in phase I). From the second phase, it has processed approx. 37.800.000 docking simulations (63 priority structures against the same 600.000 compounds). Due to the huge amount of data, only the top 20 compounds per structure (compounds with the best score hits) and based on the score function proposed by the AutoDock VINA software, have been extracted. As an example, we provided the top 20 compound which lists from the protein 1-10, 1-20 and 1-30* (See tables 1, 2 and 3)

*The notation 1-10 means the modelled structure 10, from the protein target 1 of the 53 original proteins downloaded from PDB database.

A future analysis with the high relevant results will be published in the next update of the project.

IPB Image
Figure 1. This new graph represent the current progress of the 583 priority targets (530 modelled proteins + 53 original structures) docked against the 600.000 compounds. The orange bar at the bottom of the figure represents the 53 original proteins structures already docked. The others bars represent the modelled protein structures (from 10 to 100). The blue color areas represent modelled proteins already docked and the green color areas represent the modeled proteins pending for docking. As you can see, there are 136 modelled structures still pending for docking which correspond to approximately 29%.

We want also to thank all the WCG members supporting this project all over the world, for the almost 19.000.000 results processed, out of the 1 billion data returned to the World Community Grid from IBM.


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Rilian
May 30 2013, 11:00
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Сообщение описывает с медицинской точки зрения, почему проект ищет новые варианты противодействия, несмотря на то что цены на существующие аналоги падают.

Comments on amphotericn B and why seacrhing new drugs
Dear DSFL cruncher

Amphotericin B is a drug that have been used as a second choice for the Leishmaniasis treatment in many endemic areas and with good efficay. Initially, it was administered parenterally in those patients that did not respond to the antimonials. However, it could caused severe side effects and other times it was contraindicated for certain patients. Then it was encapsulated in liposomes (a lipid bag) and the severe side effect diminished, but it was expensive. Currently, the company manufacturing this presentation cut the price and it uses as antileishmania agent have been extended. However, in spite of it decrease in toxicity and price, in this liposome presentation, the administration have to be parenteral.
It is good to know that promising studies to administer amphotericin B orally are in course at least for Visceral Leishmaniasis, which is mainly caused by two Leishmania species (Leishamnia donovani and Leishmania infantum).

We have been testing an ointment presentation of amphotericin B, with also promising results, obviously for cutaneous leishmaniasis which are approximately 1.5 million cases per year.

But why to continue searching for new drugs??. Among several reason are:
1. The number of alternative options are few. We need more or alternative options
2. The efficacy of the current drugs (included amphotericin B) can be variable depend on the Leishmania species (there are more than 20 Leishmania species associated with disease in human).
3. Development of parasite resistance when administration of amphotericin B is authorized in most endemic countries as first option, is a probability. We have to be prepared to face it.
4. The administration of amphotericin B may be contraindicated in some patients with particular condition.
5. And why to administer a systemic drug with some toxicity for treating a cutaneous ulcer?.
6. Cost may be also a reason given Leishmaniasis is mostly endemic in poor countries or affecting poor communities.
There are even more reason.

Best wishes
carmusk
Drug Search for Leishmaniasis Scientists


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Rilian
Jun 8 2013, 19:38
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07 Jun 2013

Drug Search for Leishmaniasis project update

Summary
A poster, containing preliminary Drug Search for Leishmaniasis project results, presented at the WorldLeish5 Congress in Porto de Galinhas-Brasil in May 2013.


The following Drug Search for Leishmaniasis project update can be found here .

Dear DSFL cruncher.
I am loading a poster with preliminary results from the DSFL project. This poster was presented in the past WorldLeish5 Congress in Porto de Galinhas-Brasil from May 13 to 17. Given this is the World Congress on Leishmaniasi and attended by the most important scientific working on Leishmaniasis from all over the world, I could see that none lab is doing an ambicious work like this in terms of searching new drugs for Leishmaniasis, and this has been possible for all your support as was mentioned in the acknowledge section of if. Some researchers attending the meeting and working in drug discovery were talking with me about the project and were a bit impressed. Thanks again and we are almost close to finish the project.

After we finish the computational work, we ill start the second part, which consist of filtering and selecting the potential candidates to test them in vitro and in vivo. The selection steps is based in the Autodock vina score, if the potential compound has human approval use, oral administration, cost, etc.

Best wishes and thanks

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Rilian
Jun 9 2013, 09:36
Пост #42


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Осталось менее 100 дней до завершения проекта!

Спешите заработать бейджик! koc.gif help.gif


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Rilian
Jun 18 2013, 12:04
Пост #43


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по моим подсчетам 1 фаза проекта закончится где-то через 60 дней koc.gif


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MAGADAN
Jun 18 2013, 15:30
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Что у них резкий скачет пошол вниз по дням sad.gif
И на этом проекте я могу пролететь с Сапфиром angry2.gif
Rilian если у меня щас 193 дня , и средняя 6 дней производительность я успею добраться до САПФИРА при условии что не будет разких скачков вниз по дням ?


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Я видел такое, что вам людям и не снилось!
Атакующие корабли,пылающие над Орионом!
Лучи СИ , разрезающие мрак у ворот Тангейзера!
Все эти мгновения затеряются во времени,как слёзы в дожде!
Пришло врёмя умирать!


Мне жаль небосвод этот синий,
Жаль землю и жизни осколки,
Мне страшно,что сытые свиньи,
Страшней,чем голодные волки.

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Rilian
Jun 18 2013, 15:50
Пост #45


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MAGADAN, скачки резкие будут так как в ВЦГ щяс только 2 проекта работают в полную мощность. Этот и FAAH. То есть все 400 процессорных лет в день направлены сюда.

так что я бы рекомендовал все силы сюда направить если ты планируешь добраться до бейджика


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