Posts by proxima

1) Message boards : Rosetta@home Science : CASP11 (Message 77815)
Posted 9 Jan 2015 by Profile proxima
Post:
This is excellent news - congratulations to everyone (teams members, and volunteers alike).

Nice video, too - good luck with getting to CASP12, Sergey :-)
2) Message boards : Rosetta@home Science : Selectively killing tumour cells (Message 76865)
Posted 23 Jun 2014 by Profile proxima
Post:
This seems like a pretty stunning result: From David Baker\'s Journal

We have recently made great progress in designing self assembling materials from proteins and in designing proteins which selectively kill tumor cells. These efforts have benefited tremendously from Rosetta@Home! News releases on these advances are at
http://hsnewsbeat.uw.edu/story/self-assembling-nanomachines-start-click
http://hsnewsbeat.uw.edu/story/computer-designed-protein-causes-cancer-cells%E2%80%99-death


Congratulations to all concerned :-)
3) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 75781)
Posted 20 Jun 2013 by Profile proxima
Post:
Thanks for this totally inspiring update (I\'m a recent returnee to R@H after a spell on another project).

While reading your update, my over-riding thought is how amazing it is that we (i.e. you, the scientists, or the human race in general) now know all this incredibly complex stuff, that wasn\'t known a few years ago. Whenever I read these updates about the mechanisms of proteins, bindings, targets, interactions, etc, I\'m in awe of the scientific process - and every little new thing that is learned can never be taken away from us; it\'s a step on the road that will never be undone. I really believe that complete cures will be found one day, and it\'ll be because of work like this.

Told you I found it inspiring. Thanks again for the update.
4) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4) (Message 60056)
Posted 10 Mar 2009 by Profile proxima
Post:
Thanks for these excellent and hugely motivating updates. For some of us, updates like those 5 make a real difference - please keep similar information coming as and when possible.

You should really publicise your successes more, even if just on the front page of this site. For instance, despite being a fairly committed and long-standing cruncher, I had no idea that you/we were the best-ranked group at CASP8. I\'d have that in a big banner on the front page if this was my website!

Keep up the great work.
5) Message boards : Rosetta@home Science : Design of protein-protein interfaces (Message 56778)
Posted 8 Nov 2008 by Profile proxima
Post:
I\'m very excited about this project, and look forward to your feedback.


It\'s been great getting some new \'science\' news from your and the rest of the project team. This sort of stuff is *really* motivating to a lot of us - please keep the news coming, and good luck with your project.
6) Message boards : Cafe Rosetta : Tell Wired magazine your story! (Message 55831)
Posted 17 Sep 2008 by Profile proxima
Post:
John,

I\'ve sent you a Private Message on the forum - let me know if you don\'t receive it.

Tom Reader
7) Message boards : Rosetta@home Science : Discussion on Stories from CASP8 (Message 55767)
Posted 15 Sep 2008 by Profile proxima
Post:
David has suggested that several other members of our group post in this thread as well to talk about what we did, how we did it, and tell you some hopefully amusing anecdotes about our work during CASP8. Expect those as well in the coming weeks, along with more discussions of protocols, results, and future goals for the project.


Great - there hasn\'t really been much good information coming out of the project lately (I know you are all busy)... So this is a great idea. I\'d love to hear anything about how CASP8 worked, etc, especially anything specifically to do with our work on Rosetta@Home.
8) Message boards : Rosetta@home Science : protein-protein docking at Rosetta@Home (Message 52462)
Posted 15 Apr 2008 by Profile proxima
Post:
What an excellent article - can\'t believe I missed it all that time ago, and have been wondering what CAPRI is ever since. (Although not curious enough to Google it, I guess).

Thanks for the explanation in language I can just about manage, and thanks to the various people who\'ve bumped it over the months. I have a couple of CAPRI WU\'s on the go at the momment, and it\'s great to know what they are.

Any update would be great when there\'s any news.
9) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 51910)
Posted 12 Mar 2008 by Profile proxima
Post:
That\'s really great - thanks for posting it, and thanks dcdc for putting the link back to the project. All good stuff.
10) Message boards : Number crunching : Computer array crunching? (Message 51792)
Posted 4 Mar 2008 by Profile proxima
Post:
Hi all. I was considering undergoing a goal to build an array of computers that use little power, crunch lots of data, and take up little space.


Great idea - if you get it up and running, keep us all posted - there\'d be a lot of interest I think. For example, I too have the space to store such an array, and could afford to gradually add to one, but the electricity bill is becoming the limiting factor for me.

11) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 51110)
Posted 1 Feb 2008 by Profile proxima
Post:
i think it\'d be useful if the guys could draft in a grad student or similar who could do the leg work of posting a summary if the other guys are too busy... Feedback makes a huge difference - probably more than is realised, even if it\'s just \'there\'s no real news but here\'s what we\'re working on...\'.


Yes, it\'s a good idea - there are a lot of good things about this project - and the news and feedback from the project team *used* to be one of them, but isn\'t really the case any more. As someone else said, giving us feedback as often as possible, even if it\'s only a line or two, makes a real difference.

We will be testing out new approaches to protein structure prediction in preparation for CASP8 this summer.


Yikes - another CASP already - where does the time go... Looks like it\'s going to be another hot summer in my office then!
12) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 51109)
Posted 1 Feb 2008 by Profile proxima
Post:
i think it\'d be useful if the guys could draft in a grad student or similar who could do the leg work of posting a summary if the other guys are too busy... Feedback makes a huge difference - probably more than is realised, even if it\'s just \'there\'s no real news but here\'s what we\'re working on...\'.


Yes, it\'s a good idea - there are a lot of good things about this project - and the news and feedback from the project team *used* to be one of them, but isn\'t really the case any more. As someone else said, giving us feedback as often as possible, even if it\'s only a line or two, makes a real difference.

We will be testing out new approaches to protein structure prediction in preparation for CASP8 this summer.


Yikes - another CASP already - where does the time go... Looks like it\'s going to be another hot summer in my office then!
13) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 48972)
Posted 23 Nov 2007 by Profile proxima
Post:
Exciting times!


Indeed - in fact, the two announcements that there's a "new improved" version coming along, and that virtual drug screening is also on the cards, are a couple of good bits of news. Looking forward to sticking around and helping out...

And as dcdc said, if there was any way that the results from Find-a-Drug could be used - even just as a comparison between the FaD approach and the Rosetta approach, then that would be another great use of the FaD results. I don't think the FaD results are public, or were ever intended to be, but maybe with some sort of non-disclosure agreement, the results could be used for comparison and something useful might be learned.
14) Message boards : Rosetta@home Science : evolutionary algorithm (Message 48904)
Posted 21 Nov 2007 by Profile proxima
Post:
would they work for protein folding?


If you mean a Genetic Algorithm (which I think is a bit more of a specific term), then I also wondered that here, yesterday (a few posts down in the thread). As I said there, no doubt someone somewhere has tried using a GA to help with protein folding, and I'd love to know how it went!
15) Message boards : Rosetta@home Science : Minimum energy function. (Message 48859)
Posted 20 Nov 2007 by Profile proxima
Post:
[sorry, duplicate post deleted - either this forum, or my IP connection, is REALLY grinding today].
16) Message boards : Rosetta@home Science : Minimum energy function. (Message 48858)
Posted 20 Nov 2007 by Profile proxima
Post:
I am a software engineer, if you forget that amino acids are chemicals and that sequences become proteins, and simply think of the parameters as numbers, a host of computer science techniques data mining/manipulation/etc. could be applied to this mound of data.


Me too, and that's a very interesting thought. For example, no doubt someone somewhere has tried applying Genetic Algorithms to protein folding? (GA's being a very efficient search algorithm when applied to certain kinds of problems - and needing a "fitness function" to measure the "error" of a particular solution - presumably the energy of a folded conformation would be a usable fitness function).

As I said, I'm sure this has been tried many times before by people who know far more about biology *and* Genetic Algorithms than me. Still an interesting thought though...
17) Message boards : Number crunching : Predictor of the Day stopped again (Message 46187)
Posted 14 Sep 2007 by Profile proxima
Post:
I know there have been more serious problems than this in the last few days(!), and nice one for getting the project up and running again. But can someone kick the predictor of the day setup again so it starts updating?

Thanks!

18) Message boards : Rosetta@home Science : Where we are and where we are going. (Message 46046)
Posted 12 Sep 2007 by Profile proxima
Post:
Any chance of another brief update in layman\'s terms (for example someone who doesn\'t know the difference between DNA and RNA!) as to where we are going at the moment? What are the main areas being looked into at the moment, etc?

Thanks in advance.
19) Message boards : Rosetta@home Science : Where we are and where we are going. (Message 44143)
Posted 24 Jul 2007 by Profile proxima
Post:
Agreed, it seems to have gone a bit quiet - any chance of a description of the \"big picture\" as it is at the moment, what we\'re working on, etc?
20) Message boards : Rosetta@home Science : Asthma project? (Message 42358)
Posted 20 Jun 2007 by Profile proxima
Post:
Keith is still in the Virtual Screening buisiness though and will be presenting at
..etc

That\'s great to know, thanks for that information. I didn\'t know he was still in the business, and it\'s good to know that the work we did there may still come to some use (or already has, maybe). It would be great to hear any other feedback about the outcomes from FaD.


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