Poem@Home Project

[edit] General

POEM@Home (Protein Optimization with Energy Methods) is a Boinc Project in Beta stage that is modeling the folding of protein structures.

It is a project of the Forschungszentrum Karlsruhe. The project began beta testing October 2007.

Goals of this project are:

predict the biologically active structure of proteins
understand the signal-processing mechanisms when the proteins interact with one another
understand diseases related to protein malfunction or aggregation
develop new drugs on the basis of the three-dimensions structure of biologically important proteins.

Protein simulation is presently dominated by two approaches.

You learn/copy from nature (Rosetta@Home Project). Given a new sequence, one tries to copy structural fragments of known proteins and assembles them to good structures.
- Pros: Works for big proteins, gives excellent structures for high sequence similarity.
- Cons: Does not work, when there is no sequence similarity (new folds), does not work when there is no experimental data (transmembrane proteins, to which 40% of all known drugs bind), no kinetics.

You simulate the folding process as it occurs in nature (Folding@Home) with a biophysical model. This is done with molecular dynamics (MD), an essentially sequential method with a time resolution of 10E-15 s/step. For a folding process in millisecond range you need A LOT of steps.
- Pros: full dynamics info, folding times, high accuracy structures
- Cons: works only for small proteins, specific questions

POEM tries to interpolate between these two worlds. It uses an atomistic model for the protein free energy, i.e. is can work for new folds and applications in nanobiotechnology, where there is no experimental data. In contrast to MD, it exploits Christian B. Anfinsen thermodynamic hypothesis (Nobel Prize in Chemistry 1972) that proteins in their biologically active state have a minimal free energy. The simulation process is thus replaced by an optimization process that is thousands of times faster than MD.
- Pros: Can do at least medium size proteins, gets the folding landscape, works for "new folds"
- Cons: still limited to proteins < 100 amino acids, no real kinetics (yet).

With POEM@HOME, Forschungszentrum Karlsruhe tries to make progress on these two cons.

Science:
- Results are publicly available/not-for-profit
Credits:
- Credit is granted instantly
Well-run:
- The project admins participate in the forums, and there is much info availale
- The project doesn't have a lot of outages/problems.
Other:
- The project isn't very original, there are many other protein-folding projects.
- No Screensaver yet