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> SimOne@home, В 2 словах: проект грубо говоря изучает стабильность белков в разных к
nikelong
Jan 27 2012, 02:17
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SimOne@home

Оффсайт:
http://sim1.sytes.net/sim1/

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About Simulation One
Simulation One, or SimOne@home (or even more easily SimOne), is a research project that uses Internet-connected computers to do research in the fields of science. You can participate by downloading and running a free program on your computer.

SimOne is completely created and managed by volonteers who believe in distributed computing. Our main base is of course the Boinc.Italy community from which we come. Currently we are testing the project studying the phenomenon of osmoprotection.

To investigate, here's to you some links:

Boinc.Italy web site
Osmoprotection
http://en.wikipedia.org/wiki/Osmoprotectant

Osmoprotectants

In nature, a variety of methods have been developed to allow many organisms to survive in extreme conditions such as, for example, high temperatures, high pressure or high salt concentrations. One of such method is the use of osmolytes, small molecules present even in very high concentrations in the cell fuid. Of these cosolvents in nature they are of two categories: osmoprotectant that stabilize the native structure of protein and denaturants that, on the contrary, destabilize the structure.

The mechanism of action of these molecules is still quite controversial. In fact, direct effects were observed in which the cosolvent acts directly by binding to specific sites of the protein, but were observed also indirect effects in which the cosolvent acts on the solvent changing its structure and properties and this in turn affects the protein stabilizing it or not.

The use of osmoprotectants and denaturing in the study of protein stability, both experimentally and in silico, it is very common. In particular, denaturants, such as urea, are widely used to investigate the stability of proteins, the effect of mutations on the stability and denaturation processes. Studies related to osmoprotectans are focused on the search for which molecules behave as osmoprotectans and which effects these have on proteins. Particularly studied is glycine betaine compound found in several bacterial species able to survive in extreme conditions, which is widely used in the simulations for the study of osmoprotectans. Other molecules known as osmoprotectans are some polyalcohols such as trehalose, some amino acids such as proline and betaines as the aforementioned glycine betaine.

The aim of this project is the development of a computational method capable of determining whether a molecule has an osmoprotective or denaturant effect, based on data obtained by evaluating the free energy of the process of unfolding of some polypeptide model.

The expected results for this phase should be as follows:
given a certain amount of free energy variation for the unfolding of the polypeptide in water alone, we expect a value of free energy variation is greater in cases in which the peptide was tested in the presence of osmoprotectans and less in presence of denaturants. An osmoprotectans should in fact increase the stability, and thus decrease the free energy, of folded state and this would correspond to an increase in free energy variation between folded and unfolded state, while a denaturant should decrease the stability of the folded state and then decreasing the variation free energy.

The polypeptides that are studied are two: a beta hairpin and the protein 1L2Y. The beta-hairpin was chosen as an example of beta-sheet secondary structure (length: 16 amino acids). The protein 1L2Y was chosen instead as an example of alpha helix. Special features of this protein, also called 'tpr-cage', is the fact, although very small (only 20 amino acids), it possess defined tertiary structure.

The co-solvents that are used are four: glycine betaine (GBE) and Ectoin (ECT) as osmoprotectans and urea (URE) and guanidinium chloride (GUA) as denaturant. All four compounds are fairly standard, used widely for studies in this field, both in computational and experimental.

The computational techniques that are used for calculating the free energy of unfolding are, for the moment, the umbrella sampling and Jarzynski's equation.

В 2 словах: проект грубо говоря изучает стабильность белков в разных критических условиях (температура, давление, соли)

Це повідомлення відредагував nikelong: Mar 17 2012, 17:29
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Rilian
Jan 28 2012, 13:22
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добавил описание

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Death
Jan 28 2012, 17:17
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ФФФФФФФФФФАААААААААААА


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Rilian
Jan 28 2012, 20:38
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считают программой MD run


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Rilian
Jan 29 2012, 19:24
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Посчитал 1 задание

на 3ГГц, заняло 55000 CPU сек (15.5 часов), далі 734 очка


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Rilian
Feb 25 2012, 14:32
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2012-02-24: ENG One month after the birth of the project we are pleased to announce the great strides made ??so far: 1) We have obtained stable application for Linux operating systems both 32 and 64-bit multithreaded; 2) We have the official support of the research group in Molecular Modelling, University of Milan; 3) The project is already beginning to produce results, soon I hope to write a few pages of explanation; 4) We are being developed for the application windows, even with different problems, but we're on the right path. So thanks to all of you who support this project!


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Rilian
Apr 16 2012, 17:25
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SimOne@home: Make it green!
from BOINC projects news headlines
2012-04-05: ENG Hi! Here's some news: a) As you can see WUs are rapidly declining. Indeed we are completing the first phase of the project. At this page you can see the current status and percentage completed. Make it green! b) After this phase, the server will move to a new computer that was installed and configured this month at the University of Milan. We can thus benefit from greater upload/download bandwidth and a static IP that should solve some issues with boinc client. I thank everyone for the enormous help you are giving. We reached a peak of power nearly 400 GFLOPs! Happy Easter to all! potenza! Buona Pasqua a tutti!


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Rilian
May 27 2012, 21:16
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Simulation One project moved to a new host!
The new link is http://mmgboinc.unimi.it.
Please refer to this new site for news and upgrades.
Thank you very much for your help!

Firefox can't establish a connection to the server at http://mmgboinc.unimi.it

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Rilian
Nov 21 2012, 22:26
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Есть ВЮ!

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21-Nov-2012 22:25:21 [SimOne@home] Started download of mdrun_fraction_done_4.2_lnx64
21-Nov-2012 22:25:21 [EDGI Demo Project] Sending scheduler request: Requested by project.
21-Nov-2012 22:25:21 [EDGI Demo Project] Not reporting or requesting tasks
21-Nov-2012 22:25:23 [SimOne@home] Finished download of mdrun_fraction_done_4.2_lnx64
21-Nov-2012 22:25:23 [SimOne@home] Started download of g_gyrate_4.5.5a_lnx64
21-Nov-2012 22:25:23 [EDGI Demo Project] Scheduler request completed
21-Nov-2012 22:25:26 [SimOne@home] Finished download of mdrun_4.5.5a_lnx64
21-Nov-2012 22:25:26 [SimOne@home] Started download of g_hbond_4.5.5a_lnx64
21-Nov-2012 22:25:27 [SimOne@home] Finished download of g_gyrate_4.5.5a_lnx64
21-Nov-2012 22:25:27 [SimOne@home] Started download of job_124_lnx64.xml
21-Nov-2012 22:25:28 [SimOne@home] Finished download of job_124_lnx64.xml
21-Nov-2012 22:25:28 [SimOne@home] Started download of US_ECT_0_2.7_11600.tpr
21-Nov-2012 22:25:29 [SimOne@home] Finished download of US_ECT_0_2.7_11600.tpr
21-Nov-2012 22:25:29 [SimOne@home] Started download of US_ECT_0_2.7_11600.ndx
21-Nov-2012 22:25:30 [SimOne@home] Finished download of g_hbond_4.5.5a_lnx64
21-Nov-2012 22:25:30 [SimOne@home] Finished download of US_ECT_0_2.7_11600.ndx
21-Nov-2012 22:25:30 [SimOne@home] Started download of US_ECT_0_2.7_11600.gyrate.stdin
21-Nov-2012 22:25:30 [SimOne@home] Started download of US_ECT_0_2.7_11600.hbond.stdin
21-Nov-2012 22:25:33 [SimOne@home] Finished download of US_ECT_0_2.7_11600.gyrate.stdin
21-Nov-2012 22:25:33 [SimOne@home] Finished download of US_ECT_0_2.7_11600.hbond.stdin
21-Nov-2012 22:25:33 [SimOne@home] Started download of US_ECT_0_2.7_11600.cpt
21-Nov-2012 22:25:35 [SimOne@home] Finished download of US_ECT_0_2.7_11600.cpt


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Nov 22 2012, 00:11
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Під Windows теж.
Umbrella Sampling Beta Test v0.04 (mt)


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Rilian
Nov 25 2012, 20:22
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мы на 25 месте

http://mmgboinc.unimi.it/top_teams.php?sor...redit&offset=20


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Death
Nov 25 2012, 20:51
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К сожалению, Google Chrome не может найти страницу sim1.sytes.net.
Попробуйте:
Перейдите на страницу sytes.­net
Перейти к карте сайта sytes.­net/­site_map.­php
Искать в Google:


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Death
Nov 27 2012, 00:10
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25.11.2012 20:54:24 | SimOne@home | Project has no tasks available
25.11.2012 21:10:18 | SimOne@home | Sending scheduler request: To fetch work.
25.11.2012 21:10:18 | SimOne@home | Requesting new tasks for CPU
25.11.2012 21:10:20 | SimOne@home | Scheduler request completed: got 1 new tasks
25.11.2012 21:10:22 | SimOne@home | Started download of wrapper_25825_windows_intelx86.exe
25.11.2012 21:10:22 | SimOne@home | Started download of mdrun_4.5.4a_win32.exe
25.11.2012 21:10:24 | SimOne@home | Finished download of wrapper_25825_windows_intelx86.exe
25.11.2012 21:10:24 | SimOne@home | Started download of g_gyrate_4.5.4a_win32.exe
25.11.2012 21:10:27 | SimOne@home | Finished download of g_gyrate_4.5.4a_win32.exe
25.11.2012 21:10:27 | SimOne@home | Started download of g_hbond_4.5.4a_win32.exe
25.11.2012 21:10:28 | SimOne@home | Finished download of mdrun_4.5.4a_win32.exe
25.11.2012 21:10:28 | SimOne@home | Started download of cygwin1_1.7.10a_win32.dll
25.11.2012 21:10:30 | SimOne@home | Finished download of g_hbond_4.5.4a_win32.exe
25.11.2012 21:10:30 | SimOne@home | Started download of job_3_win32_mt.xml
25.11.2012 21:10:32 | SimOne@home | Finished download of job_3_win32_mt.xml
25.11.2012 21:10:32 | SimOne@home | Started download of US_GUA_0_0.6_12900.tpr
25.11.2012 21:10:33 | SimOne@home | Finished download of cygwin1_1.7.10a_win32.dll
25.11.2012 21:10:33 | SimOne@home | Started download of US_GUA_0_0.6_12900.ndx
25.11.2012 21:10:34 | SimOne@home | Finished download of US_GUA_0_0.6_12900.tpr
25.11.2012 21:10:34 | SimOne@home | Started download of US_GUA_0_0.6_12900.gyrate.stdin
25.11.2012 21:10:35 | SimOne@home | Finished download of US_GUA_0_0.6_12900.ndx
25.11.2012 21:10:35 | SimOne@home | Finished download of US_GUA_0_0.6_12900.gyrate.stdin
25.11.2012 21:10:35 | SimOne@home | Started download of US_GUA_0_0.6_12900.hbond.stdin
25.11.2012 21:10:35 | SimOne@home | Started download of US_GUA_0_0.6_12900.cpt
25.11.2012 21:10:36 | SimOne@home | Finished download of US_GUA_0_0.6_12900.hbond.stdin
25.11.2012 21:10:37 | SimOne@home | Finished download of US_GUA_0_0.6_12900.cpt
25.11.2012 21:10:42 | SimOne@home | Starting task US_GUA_0_0.6_12900_1 using us version 125 (mt) in slot 2
25.11.2012 23:13:52 | SimOne@home | Sending scheduler request: To fetch work.
25.11.2012 23:13:52 | SimOne@home | Requesting new tasks for CPU
25.11.2012 23:13:54 | SimOne@home | Scheduler request completed: got 0 new tasks
25.11.2012 23:13:54 | SimOne@home | Project has no tasks available
25.11.2012 23:48:54 | SimOne@home | Computation for task US_GUA_0_0.6_12900_1 finished
25.11.2012 23:48:57 | SimOne@home | Started upload of US_GUA_0_0.6_12900_1_0
25.11.2012 23:48:57 | SimOne@home | Started upload of US_GUA_0_0.6_12900_1_1
25.11.2012 23:49:00 | SimOne@home | Finished upload of US_GUA_0_0.6_12900_1_0
25.11.2012 23:49:00 | SimOne@home | Finished upload of US_GUA_0_0.6_12900_1_1
25.11.2012 23:49:00 | SimOne@home | Started upload of US_GUA_0_0.6_12900_1_2
25.11.2012 23:49:00 | SimOne@home | Started upload of US_GUA_0_0.6_12900_1_3
25.11.2012 23:49:01 | SimOne@home | Finished upload of US_GUA_0_0.6_12900_1_3
25.11.2012 23:49:04 | SimOne@home | Finished upload of US_GUA_0_0.6_12900_1_2
25.11.2012 23:49:08 | SimOne@home | Sending scheduler request: To report completed tasks.
25.11.2012 23:49:08 | SimOne@home | Reporting 1 completed tasks


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Rilian
Jul 19 2013, 10:39
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Опубликовали статью

http://www.sciencedirect.com/science/artic...00926141300763X


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