birdman2584
10-15-2005, 08:12 AM
Taken from the Rosetta Site and written by david baker, lead scientist guy
The past few weeks have been incredibly exciting for us as we have watched all of you explore protein folding landscape far too large to adequately map out using traditional computing methods. As often happens in scientific research, we didn't find what we expected. We had hoped that with the amount of computing power you all are bringing to bear on the problem, it might be possible to find the global energy minimum at the experimentally observed structure (rmsd close to zero). Instead, as you can see from the plots that David has posted for the four protein landscapes you have investigated so far, nobody has yet to land within 1 rmsd of the actual structure. To solve this problem we need to improve our search methods, and you need to recruit more crunchers. We will return to these four proteins in several months by which time I'm optimistic that both we and you will have done what is necessary to solve these four problems perfectly. I should say, however, that the 2 rmsd models that you have found in the past weeks are quite close to the correct structures, as you can see in the pictures, and would be accurate enough for understanding how the proteins work. For the next month we will be focusing on improving our sampling methods on smaller proteins, and, due to the decreased size and also due to efforts made by the rosetta community across the country to reduce the memory requirements in response to your concerns, you should see considerably lower memory usage.
I think it's pretty interesting and always good to get an update on what is going on! I strongly recommend this project to anyone who gets bored if they dont get updates.:thumbs: :thumbs: 2 thumbs up!
The past few weeks have been incredibly exciting for us as we have watched all of you explore protein folding landscape far too large to adequately map out using traditional computing methods. As often happens in scientific research, we didn't find what we expected. We had hoped that with the amount of computing power you all are bringing to bear on the problem, it might be possible to find the global energy minimum at the experimentally observed structure (rmsd close to zero). Instead, as you can see from the plots that David has posted for the four protein landscapes you have investigated so far, nobody has yet to land within 1 rmsd of the actual structure. To solve this problem we need to improve our search methods, and you need to recruit more crunchers. We will return to these four proteins in several months by which time I'm optimistic that both we and you will have done what is necessary to solve these four problems perfectly. I should say, however, that the 2 rmsd models that you have found in the past weeks are quite close to the correct structures, as you can see in the pictures, and would be accurate enough for understanding how the proteins work. For the next month we will be focusing on improving our sampling methods on smaller proteins, and, due to the decreased size and also due to efforts made by the rosetta community across the country to reduce the memory requirements in response to your concerns, you should see considerably lower memory usage.
I think it's pretty interesting and always good to get an update on what is going on! I strongly recommend this project to anyone who gets bored if they dont get updates.:thumbs: :thumbs: 2 thumbs up!