Announcement

**High_Jumbllama** · 8 January 2003, 17:23

Is the new screensaver faster? I seem to be getting 700 seconds or 11 minutes 40 seconds per 1000 folds which is .7 secs per fold. Or is it just the smaller protein size. I do like this screensaver much more than the last version. If only it didn't look hideous but I'd rather have the performance anyway.

I turned the graphics down all the way and checked the extra ram option.

All this on the machine in my sig.

**Guru** · 23 January 2003, 16:08

01/22/2003

- We are fast approaching 10 billion again, and have a 6.5A structure! So congratulations to all. This particular protein was expected to get roughly a 6A structure in a sample of 10 billion so we have come very close to that prediction. We will be changing proteins again next Tuesday afternoon, EST. Also coming soon, a brand new smarter algorithm. Watch here and in the discussion forum for details.

- Results from the CASP5 structure prediction competition have been posted in the results section, with a brief explanation of how to interpret the graphs. In most cases our predictions were in the middle of the pack. This might not sound as good as we had hoped, but it means none of our predictions were THAT bad, and in general all five of our top predictions were of comparable quality, meaning that we were picking out structures consistently. It is also important to keep in mind that of the 13 targets predicted, only T0129, T0139, T0161 and T0181 were truly 'new folds'. Other targets could in some cases be predicted by other means starting from related known structures (though still by no means easy to predict). We still need to go through the structures we generated to see if we submitted the best predictions we could have, or if there were better structures that our scoring function simply failed to pick out. Clearly brute force alone is not sufficient to beat other more intelligent search methods though, and we will shortly be revising the algorithm to work in a more intelligent, iterative sampling approach, which we expect to have a huge effect on the overall performance and efficiency of the sampling.

**Guru** · 23 January 2003, 16:11

Coming Soon page also updated! Not sure about the Known Bugs and Workarounds page!

**Guru** · 28 January 2003, 12:32

01/28/2003

- We will be switching proteins at about 3PM EST today. The new algorithm that we have been developing is now being 'alpha tested' and will be released for beta testers to thoroughly test within the next few weeks. If interested in being a beta tester, please keep an eye on the Discussion Forum.

**Guru** · 28 January 2003, 16:16

New protein is up!

http://www.distributedfolding.org/Download.html In case you are not using the autoupdate function!

**High_Jumbllama** · 28 January 2003, 19:43

This one is a little small. Good for a light nutritious snack. I just wish the auto-update would work on the screensaver.

**Guru** · 3 February 2003, 13:38

DF on PS2!

01/31/2003

- A few announcements - firstly, fo anyone who downloaded the UNIX client directly from the Download page of the web site since this Tuesday, please note that some switches were accidentally set wrong in the foldit script. Please check the foldit script and ensure the '-if' flag is not present unless you wanted it to be (see the Readme for details on what each flag does)

- An updated version of the software has been released (only the protein was updated on Tuesday) which fixes a number of minor issues, so grab the new verison if any of these affect you: time and date stamps are added in the error.log for some network errors; updates might be detected better behind transparent proxy servers now; and a bug in reading the foldtraj_fileserver.cfg file (when using the update proxy daemon) was corrected.

- Lastly, and most importantly, we have yet another two ports! By popular request we've released a 32-bit IRIX client. We've also released a Sony Playstation 2 Linux client. This requires Sony's 'Linux Kit', available for purchase at www.playstation.com, and has not been specifically optimized for the CPU so it runs a little slow. Head over to the Download section to get these of course.

http://www.distributedfolding.org/news.html

**High_Jumbllama** · 3 February 2003, 16:12

Re: DF on PS2!

Originally posted by Guru
01/31/2003

- Lastly, and most importantly, we have yet another two ports! By popular request we've released a 32-bit IRIX client. We've also released a Sony Playstation 2 Linux client. This requires Sony's 'Linux Kit', available for purchase at www.playstation.com, and has not been specifically optimized for the CPU so it runs a little slow. Head over to the Download section to get these of course.

http://www.distributedfolding.org/news.html

PS2 Incredible but then again I suppose it would mostly be a matter of recompiling.

**Guru** · 17 February 2003, 02:09

02/16/2003

- Patented - we are proud to announce the the Distributed Folding structure generation algorithm is now patented (U.S. Patent no. 6490532, as of Dec. 3, 2002). For details, visit the patent office here.

http://distributedfolding.org/news.html

**Guru** · 19 February 2003, 14:57

02/19/2003

- Beta-testing has begun for our new sampling algorithm. Windows and Intel Linux versions are available for interested parties. If you wish to help beta-test the software, please visit the Discussion Forum for detailed information on how to get the beta software and help.

- The next protein update will occur next Tuesday, Feb. 25 provided we have passed the 10 billion mark by that point

http://www.distributedfolding.org/news.html

Oh and btw the protein should change again next week!

**Guru** · 27 February 2003, 07:55

02/26/2003

- At approximately 10PM EST late last night, some currently unknown set of circumstances caused the main database storing user and structure data to become corrupted. Luckily minimal work was lost because we had just switched to a new protein hours before. Unfortunately the only way we could remedy the situation was to re-create the database from scratch. All user data (including stats, total number of structures built, etc.) has been preserved as of the time of the protein change. As a minor side effect, the user id numbers (UIDs), which some people use to track users who do not have names, MAY not be preserved in some cases and may have in fact changed now. Other than that, all teams, your e-mails, passwords, and so on should be fine. In light of the failure, you will be allowed to upload the previous protein for credit for 24hrs from this point on (9PM EST) and for 48 hrs for half credit. As always, your patience and understanding is appreciated and we apologize for any inconvenience this may have caused. Please note that if you registered as a new user yesterday, you may need to register again - try logging in on the High Flyers page, and if it does not recognize your e-mail, you will need to sign up once more.

02/25/2003

- We have released a new protein again today. One important note though. The Windows and linux-i386 files on the FTP site (i.e. if you go to the Download page and click the links) included the incorrect executables (the Beta versions). This is fixed now (as of 11:20PM EST) so if you downloaded the incorrect copy, please try again now (make sure your browser doesn't cache the download and it really re-downloads it). If unsure, run 'foldtrajlite' from the command line with no arguments. the date on the first line should be Jan 31. If instead it is a date in Feb., you have the beta. If your machine auto-updated you won't have this problem. Sorry for any trouble this may have caused.

**Guru** · 18 March 2003, 08:29

03/17/2003

- Screensaver bug - a bug has been discovered in the Windows screensaver. If you change any of the settings in the Configuration dialog box, you will lose any progress made since the last upload. This is mostly a problem for people who run the program offline with 'do not connect to internet' checked off, and then uncheck this to upload. For details see the bugs page. It will be fixed in the next release.

**Guru** · 1 April 2003, 11:52

04/01/2003

- Due to circumstances beyond our control, the protein change that was scheduled for today will not occur. We will continue to work on the current protein until further notice. Check back here frequently if concerned, or else just wait for your machine to detect the next update when it becomes available. Beta testing of teh new algorithm will proceed as normal.

http://www.distributedfolding.org/news.html

**Guru** · 3 April 2003, 07:54

Update!

04/03/2003

- Protein update will be occuring at approx. 3pm EST today, Thursday.

http://distributedfolding.org/news.html

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