- Feb 15, 2001
- 9,673
- 1
- 81
From David Baker, the lead researcher:
From analyzing the results of the searches all of you have done over the past week we have made a real breakthrough! The puzzle that emerged at the end of last week was that, while very low rms structures were generated in your searches, they typically had much higher energies than the native structure. It was as if you were playing golf, and the hole you were trying to land in was surrounded by an elevated barrier. I was puzzling over this while bicycling up the hill behind my house Sunday morning, and had an idea which I incorporated into the program and tested later in the day. The really neat result is that when I took the lowest rmsd structures that you found, and started calculations from them, the energy dropped dramatically, and the rmsd decreased significantly as well, as if the barrier had been replaced by a gentle slope down into the hole. Since Sunday, Vatson, a graduate student, Bin, a postdoctoral researcher in my group, and I have found that this dramatic movement towards the native structure occurs for a number of different protein systems.
David Kim is now preparing the latest version of the code for distribution on BOINC, and you will hopefully receive work units with the improved algorithm sometime tomorrow. If he has time, David will include the graphics option Jack Schonbrun has developed which shows quite vividly what is going on during the calculations. We think it is going to be a hit!
From analyzing the results of the searches all of you have done over the past week we have made a real breakthrough! The puzzle that emerged at the end of last week was that, while very low rms structures were generated in your searches, they typically had much higher energies than the native structure. It was as if you were playing golf, and the hole you were trying to land in was surrounded by an elevated barrier. I was puzzling over this while bicycling up the hill behind my house Sunday morning, and had an idea which I incorporated into the program and tested later in the day. The really neat result is that when I took the lowest rmsd structures that you found, and started calculations from them, the energy dropped dramatically, and the rmsd decreased significantly as well, as if the barrier had been replaced by a gentle slope down into the hole. Since Sunday, Vatson, a graduate student, Bin, a postdoctoral researcher in my group, and I have found that this dramatic movement towards the native structure occurs for a number of different protein systems.
David Kim is now preparing the latest version of the code for distribution on BOINC, and you will hopefully receive work units with the improved algorithm sometime tomorrow. If he has time, David will include the graphics option Jack Schonbrun has developed which shows quite vividly what is going on during the calculations. We think it is going to be a hit!
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