Protein related projects

[tutta55]

From the SIMAP forum:

- Rosetta@Home
information about the project given at http://boinc.bakerlab.org/rosetta/rah_research.php

Quote:
The goal of our current research is to develop an improved model of intra- and intermolecular interactions and to use this model to predict and design macromolecular structures and interactions. Prediction and design applications, which can be of great biological interest in their own right, also provide stringent and objective tests that improve the model and increase fundamental understanding.
We use a computer program called Rosetta to carry out protein and design calculations. At the core of Rosetta are potential functions for computing the energies of interactions within and between macromolecules, and methods for finding the lowest energy structure for an amino acid sequence (protein-structure prediction) or a protein-protein complex and for finding the lowest energy amino acid sequence for a protein or protein-protein complex (protein design). Feedback from the prediction and design tests is used continually to improve the potential functions and the search algorithms.


- Predictor@Home
information about project given at: http://predictor.scripps.edu/about_plan.php

Quote:
Our short term plan for Predictor@Home is to test and evaluating new algorithms and methods of protein structure prediction. In the near term we will be calibrating the P@H methods against a set of known structures. In the longer term we hope to open Predictor@Home up to the community as a resource to assist in protein structure prediction.


- World Community Grid

Quote:
The Human Proteome Folding Project will combine the power of millions of computers in a grid to help scientists understand how human proteins fold. The work to be done in this monumental task is shared across this grid, so that results can be achieved far sooner than would be possible with conventional supercomputers. With a greater understanding of protein structure, scientists can learn how diseases work and ultimately find cures for them. When your grid agent is running, it is folding an amino acid chain in various ways and evaluating how well each folding follows the specific rules of how specific amino acids stick together or not. As computers try millions of ways to fold the chains, they attempt to fold the protein in the same way that it actually folds in the human body. The best shapes identified for each protein are returned to the scientists for further study. The name of the computer program is Rosetta. It computes a "Rosetta score" that tells how properly folded a protein is as the program tries different foldings. To compute this score, the program considers the packing of amino acids within the protein according to many scoring rules. The lower (more toward the negative) the scores are, the better the folding.


- Folding@Home

Quote:
To solve the protein folding problem, we need to break the microsecond barrier. Our group has developed multiple new ways to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way -- with a near linear speed up in the number of processors. Thus, with power of Folding@Home (over 100,000 processors), we have successfully smashed the microsecond barrier, simulating milliseconds of folding time and helped to unlock the mystery of how proteins fold.


- SIMAP@Home

Quote:
What is SIMAP?
SIMAP is a database of protein similarities. It contains about all currently published protein sequences and is continuously updated. Protein similarities are computed using the FASTA algorithm which provides optimal speed and sensitivity. SIMAP is to our knowledge the only project that combines comprehensive coverage with respect to all known proteins and incremental update capabilities.


To get to the point: Rosetta/Predictor/WGC/Folding@Home test protein folding (best chemical structure) - SIMAP is going to analyze the existing databases (based on the FASTA-algorithm) to detect sequence similiarities (homologs). Probably proteins with similar amino acid sequences show the same or related functions. A FASTA-Query consists of four parts: Hashing, Scoring 1 + 2 and Alignment (detailed information follow). Goal of the sequence alingment is to find similiarities of phylogenies and protein-function.

[Spacejuice]

wel, om nu ni veel te zeggen,...

veel wijzer ben ik er nu ook niet uit geworden....

Dat verdient toch een reputationpointje voor de uitleg te verzamelen!!

[Skatoony]

Quite a bit of information there.

[tutta55]

Ok, after an explanation that was much too long, here's another one that may be much too short

- Predictor: Searches for new ways to predict protein structure.
- Rosetta: Tries to improve the Rosetta method for predicting and designing protein structure.
- WCG: Uses the existing Rosetta method as it is.
- SIMAP: Will make a database of similarities between different proteins.
- Folding: Also predicts protein structure. Boinc-ers not too welcome afaik.

They are active in the same area, but that doesn't mean they do the same work. Which one too choose? That is a matter of personal taste. All may finally come up with results that can lead to new medecins or a better understanding of disease. Personally I prefer Rosetta for the moment, because the project leaders are responsive and active in their own forum.

[Spacejuice]

Well, that's much better than the long texts you posted earlier.

Thanx a lot!

[Saenger]

RNA World
En nieuwe project uit de omgeving van Rechenkraft.

About RNA World (beta)
RNA World (beta) is a distributed supercomputer that uses Internet-connected computers to advance RNA-related research. You can participate by downloading and running a free program on your computer.

RNA World (beta) is based at the Rechenkraft.net e.V. research facility located in Germany.

* Projectdescription
* Project location & personnel
* Cooperation partners
* Sponsors
* FAQ
* Presentation of the project at the 5th Pan-Galactic BOINC Workshop

[Annabel]

Ziet er de max uit Saenger! Ik ben benieuwd of en waar ik kan bijdragen (ik vind de link daarvoor niet direct op de website van Rechenkraft).

[Saenger]

Originally Posted by Annabel

Ziet er de max uit Saenger! Ik ben benieuwd of en waar ik kan bijdragen (ik vind de link daarvoor niet direct op de website van Rechenkraft).

Er zijn 9 links in mijn post
Maar de project is tot nu nog closed beta, BOINC.BE heeft al en team en tutta en account. Ik hoop, dat Yoyo en Michael gauw de project helemaal open doen, niet alleen voor de oprichter van de BOINC-wide teams.

http://www.rnaworld.de/rnaworld/

[Saenger]

Lang niet hier geweest
De project is nu open voor iedereen, niet allen maar oprichters. Er is niet altijd werk, omdat soms voor en nieuwe batch eerst de oude moet gedaan worden, maar de meeste tijd zou er volgens de admin wel werk zijn