Posts by Possu

1) Message boards : Rosetta@home Science : Designing exciting new artificial enzyme scaffolds (Message 79831) Posted 1 Apr 2016 by Possu Post: The triosephosphate isomerase barrel fold (TIM barrel fold) is one of the most widely used enzyme fold in nature. We recently succeeded in creating a de novo TIM barrel -- the first of its kind. Now we want to build on what we have learned and expand the diversity of the structures for new artificial enzymes! The structure consists of of 8 strands and 8 helices. The 8 strands come together to form a barrel on the inside of the protein, and the helices are on the exterior to complete this two ring structure. we initially set it up with 4-fold symmetry to try to understand the fold. Now a new batch of calculations on Rosetta@Home are testing 2-fold symmetric setup. They look like two half circles trying to find ways to reach a full circle (barrel)! here's a recent C&EN coverage on the project. http://cen.acs.org/articles/93/i47/Protein-Designers-Roll-Barrel.html
2) Message boards : Number crunching : How much has your RAC Dropped Since 12/6/06 (Message 34467) Posted 10 Jan 2007 by Possu Post: Boinc expects all the work units take the same amount of time. The credit system fluctuates in the beginning and averages out over time. Because some of the jobs for the looprlx are short and likely finished before the stats can stabilize, it is the nature of this type of jobs. The jobs run without any problem.
3) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (2) (Message 28130) Posted 21 Sep 2006 by Possu Post: They are easier problems. Because the HIV protein is quite large, we are modeling it in smaller chunks, only one loop at a time (usually only 5-10 amino acids long). So if you happen to get one of those calculations, you will notice that the structure showing in the graphics window/screen saver looks like discontinuous fragments. That's the region we are refining at the moment. Bigger chunks will come later. Also people will probably notice that the structure doesn't move much because a lot of the movements are occuring on the sidechain level and rosetta@home haven't has the ability to show sidechains yet. Thanks for all the cpu time. It's exciting to see the 'PSH......' Work Units coming. An interesting early effect has been seen in that at least some of these Work Units generate a substantially larger number of decoys per unit CPU time than other recent WUs such as the CASP refinements, LARS runs, or 'FARELAX...' cases. Is there something about the structure of these 'PSH' proteins that induces that effect?
4) Message boards : Rosetta@home Science : Rosetta@home Active WorkUnit(s) Log (Message 27652) Posted 20 Sep 2006 by Possu Post: We are now using Rosetta@Home to screen our HIV vaccine designs. We are remodeling the protein called GP120, which is responsible for binding with human proteins and initiate the invasion to host cells. The remodeled/redesigned GP120 can potentially be used as a vaccine. (Please see David's journal for more info) The jobs submitted for this will have a prefix "PSH" and future jobs will also carry the name(s) GP120 and OD1 (stands for the outer domain of the GP120) for easy identification. We are using the jobs on Rosetta@Home to refold and refine the sequences came from design runs. We first remodel the backbone using rosetta (~2000+ different backbone conformations), design them to put suitable sequences on for each of the conformations, and then score all these different sequences to find the best ones to test experimentally. The scoring process is very time consuming as each of the 2000+ starting conformations will have to be sampled thoroughly in its local conformational space before we can call definitively which is the best designed sequence. That's when Rosetta@Home comes to the rescue...