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1) From CASP we learned that POEM is really great in quality assessment. On this basis we will implement a continues web-service, which biologist can use to assess protein structure.
2) We also learned that our protocol did not generate enough new structures in the de novo fold category. So in the next two years we will work hard to improve this protocol for the next CASP.
3) We have already succeeded (with POEM@HOME) to identify a gene responsible for a late-stage developmental disorder. This affects 1 in 10000 births, so we are very proud to develop analysis tools that actually help people right now. Obviously we will strive to continue this effort. (results update coming soon).
4) We will go back to the folding studies: POEM@HOME has folded several proteins, but now that CASP is over, we will go back to improving these algorithms.
5) .... 99) Many more ideas, not enough manpower. We keep you posted.
sanhaji wrote:1) From CASP we learned that POEM is really great in quality assessment.
1) Aus CASP hat man gelernt, dass die Stärken von POEM in der Qualitätsbestimmung von Proteinen liegt (Verbesserung existenter Strukturen)
So first of all two targets, which we did good and bad at:
One target we are quite proud of is T0423
If you look at all the submitted models of this target, we come out first:
As POEMQA did refinement of the input structure, this means, that our way to refine really worked, as the structure is better than any of the ones we used as input.
One of the targets, which I found really interesting was target T0401:
T0401. POEMQA submitted a bad model (GDT-TS 27/100) and a good model (GDT-TS 65/100).
As the simulated energy of the bad model was quite a bit 'better' for the bad model, we investigated why this happened, as afterall there were structures of good topology in the populations we rated. It occurs, that T0401 naturally occurs as a dimer, so two of the same proteins are adjacent to each other; we however started the simulation from a monomer, because it was not known, that the protein occurs as a dimer before CASP.
The interesting part here now is, that if the protein would be isolated, our conformation could really be lower in energy, the interaction energy between the two domains however stabilizes the structure.
As I already said, overall the participation of POEM and POEMQA was a success. POEMQAs results were better than those of POEM, because most of the time POEMQA had access to populations of starting structures, which were already nearer the native structure.
Häufig wurde vom Robetta Server eine Struktur abgegeben, die besser als die POEM Strukturen war. Das ist hauptsächlich der Fall, weil Robetta in der ersten Strukturgenerierung besser ist als die Methoden, die wir vor dem Submit auf POEM@HOME zur Generierung verwenden.
Wenn wir nicht gerade bei CASP teilnehmen falten wir bei POEM ja meist "von 0" und suchen dann den Raum der interessanten Strukturen ab, dementsprechend benötigen wir da keine Startstrukturen ausser der komplett ausgedehnten.
Unsere Teilnahme war aber dennoch ein voller Erfolg, weil der Refinement-schritt auf POEM@HOME, der für unsere normalen Simulationen der wichtigste ist, immer gut funktioniert hat.
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