WCG

[Heyoka]

Y a de la littérature scientifique à traduire  

http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=7703

HI FROM THE NYU CENTER FOR COMPARATIVE FUNCTIONAL GENOMICS!
ok, i'm a bit excited ...

HPF2 is launched. This is very exiting to me and to my lab members. We've been working with IBM for a while now and were very excited when they told us that we could put this project on the grid.

HPF2 is different from HPF1, but in a way that might not mean much to those who don't think about structure prediction. HPF2 is a higher resolution version of HPF1. In HPF1 we modeled the protein at the level of overall shape (each part of the molecule was represented by a few atoms). In HPF2 we try to model all atoms in the protein and use a mode of Rosetta that pays attention to roughly twice the number of atoms modeled in HPF1. This means we have to spend more compute time per protein and that we have to narrow our focus for HPF2.

If you're new to HPF then check out the FAQ for HPF2 and HPF1. There is a lot of information in the descriptions of HPF2 that refers back to HPF1 so check out the HPF1 faq and description first if your interested.

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more details:
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HPF phase II:

HPF phase-2 will refine, using Rosetta in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the Human Proteome Folding Project (HPF phase1). The project will focus on human secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the pro-teins). The project will also focus on key secreted pathogenic protein. This project dove-tails with efforts at the ISB in Seattle to support predictive, preventative and personalized medicine (under the assumption that these secreted proteins will be key elements of this medicine of the future).

This project continues where the Human Proteome Folding Project leaves off. With the Human proteome Folding project we aimed to get protein function. With the second phase we would aim to increase the resolution of a select subset of Human proteins. Better reso-lution is important for a number of applications including but not limited to virtual screening of drug targets with docking procedures and protein design. The second phase of the pro-ject will also serve to improve our understanding of the physics of protein structure and ad-vance the state of the art in protein structure prediction (help us to further develop our program, Rosetta).

The two main objectives are to: 1) obtain higher resolution structures for specific hu-man proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta structure prediction. Thus, the project would ad-dress two very important parallel imperatives, one biological and one biophysical.

The Human Proteome Folding Project Phase-2 will use the computer power of millions of computers to predict the shape of Human proteins for which researchers currently know little. From this detailed shape scientists hope to learn about the function of these proteins, as the shape of proteins is inherently related to how they function in our bodies. This data-base of protein structures and putative functions will let scientists take the next steps un-derstanding how diseases that involve these proteins work. Proteins are the most important molecules in living beings. Just about everything in your body involves or is made out of pro-teins. Protein structure is key to understanding the functions of this diverse class of bio-molecule. Thus we hope that our work on HPF 1 and HPF 2 will contribute to critical pub-lic infrastructure to the biological and biomedical community.

https://secure.worldcommunitygrid.org/projects_showcase/viewHpf2Research.do

Human Proteome Folding - Phase 2     

Human Proteome Folding Phase 2 (HPF2) continues where the first phase left off. The two main objectives of the project are to: 1) obtain higher resolution structures for specific human proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta software structure prediction. Thus, the project will address two very important parallel imperatives, one biological and one biophysical.

The project, which began at the Institute for Systems Biology and now continues at New York University's Department of Biology and Computer Science, will refine, using the Rosetta software in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the project. The goal of the first phase was to understand protein function. The goal of the second phase is to increase the resolution of the predictions for a select subset of human proteins. Better resolution is important for a number of applications, including but not limited to virtual screening of drug targets with docking procedures and protein design. By running a handful of well-studied proteins on World Community Grid (like proteins from yeast), the second phase also will serve to improve the understanding of the physics of protein structure and advance the state-of-the-art in protein structure prediction. This also will help the Rosetta developers community to further develop the software and the reliability of its predictions.

The project also will focus on key secreted pathogenic proteins. While still in its early design phases, HPF2 will likely focus on Plasmodium, the pathogenic agent that causes malaria. Researchers hope that higher resolution structure predictions for the proteins that malaria secretes will serve as bioinformatics infrastructure for researchers who are working hard around the world to understand the complex interaction between human hosts and malaria parasites. While there are few silver bullets, and biology is one of the most complicated subjects on earth, researchers believe that this work will help it understand elements of this host-pathogen interaction or at least its components. Researchers will provide their findings as a resource to the scientific community and then work with the community on visualizing, using and refining the data. This understanding could then be a foundation for intervention.

HPF2 will focus on human-secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the proteins). Examples of human secreted proteins turned into therapeutics are insulin and the human growth hormone. Understanding the function of human secreted proteins may help researchers discover the function of proteins of unknown function in the blood and other interstitial fluids.

The project also will focus on key secreted pathogenic proteins. While still in its early design phases, HPF2 will likely focus on Plasmodium, the pathogenic agent that causes malaria. Researchers hope that higher resolution structure predictions for the proteins that malaria secretes will serve as bioinformatics infrastructure for researchers who are working hard around the world to understand the complex interaction between human hosts and malaria parasites. While there are few silver bullets, and biology is one of the most complicated subjects on earth, researchers believe that this work will help it understand elements of this host-pathogen interaction or at least its components. Researchers will provide their findings as a resource to the scientific community and then work with the community on visualizing, using and refining the data. This understanding could then be a foundation for intervention.

Lastly, this project dovetails with efforts at NYU and ISB to support predictive, preventative and personalized medicine (under the assumption that these secreted proteins will be key elements of this medicine of the future). It is too early to say which proteins will end up being biomarkers (substances sometimes found in an increased amount in the blood, other body fluids, or tissues and which can be used to indicate the presence of some types of cancer). However, it is clear that many will end up being secreted proteins. As in the first phase of the project, the power of World Community Grid will be critical in getting results quickly to researchers in the biological and biomedical communities.

For more information about proteome folding, click here.

Ensuite si on arrive à traduire tout ça, il y aura ça
http://www.worldcommunitygrid.org/projects_showcase/viewHpf2Faq.do?shortName=hpf2

[Heyoka]

J'ais dejà fait ça

BONJOUR, DU CENTRE DE NYU POUR LA GÉNOMIQUE FONCTIONNELLE COMPARATIVE !
ok, je suis très ému

La HPF2 vient d'être lancée. L'effervescence est à son comble en ce qui me concerne ainsi que pour les membres du laboratoire. Nous avions travaillé pendant un moment avec IBM et nous avons été très émus quand ils nous ont dit que nous pourrions mettre ce projet sur la grille de cacul

La HPF2 est différente de la HPF1, mais d'une manière qu'il est difficile d'expliquer pour à ceux qui ne connaissent très peu en matière de protéomique. HPF2 est une version disposant d'une meilleure résolution que HPF1. Dans HPF1 nous avons modelé la protéine au niveau de sa forme globale (chaque partie de la molécule a été représentée par quelques atomes). Dans HPF2 nous essayons de modeler tous les atomes de la protéine et d'employer une fonction de Rosetta qui analyse deux fois le nombre d'atomes modelés dans HPF1. Ceci signifie que nous allons devoir orienter plus de temps de calcul par protéine et pour arriver à cela nous devons rétrécir notre champ de recherche pour HPF2.

Si vous êtes nouveau sur HPF, jetez un coup d'oeil à la FAQ HPF2 et HPF1. Il y a beaucoup d'information dans la description de la HPF2 qui renvoie à la HPF1 ainsi si vous êtes intéressé vous pouvez vous diriger vers la FAQ de la HPF1

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Phase II de HPF :