Posts by Hoelder1in

41) Message boards : Cafe Rosetta : Rosetta Banner? (Message 19761)
Posted 4 Jul 2006 by Profile Hoelder1in
Post:
Here is another one. This one was designed by Simon Smith, owner and manager of the betterhumans.com website, to promote the betterhumans Rosetta@home team (it appears in place of the Google banner at betterhumans.com whenever Google doesn't have anything else to display). For general Rosetta@home promotion the reference to the betterhumans team would of course have to be removed. But I think it still is interesting as a design example. The background is meant to symbolize the benefit of determining/designing protein structures (left) for humans (right).



I would have to ask Simon whether he wants to make this available for general Rosetta@home promotion.
42) Message boards : Number crunching : There is nothing in my Team page. Why? (Message 18807)
Posted 16 Jun 2006 by Profile Hoelder1in
Post:
I use IE, when I click on EspiTeam (Spain - Espań”©¼/a>, I get a blank page.
tony

Hm...I get a '?' instead of the 'n' in Espana. Perhaps you should try ñ instead whatever you typed for the 'n' ? At least I hope that's the right sign...
43) Message boards : Rosetta@home Science : Designing proteins and enzymes (Message 18504)
Posted 12 Jun 2006 by Profile Hoelder1in
Post:
I wanted to point you to a post I made in another forum that discusses the protein and enzyme design capabilities of Rosetta, quoting some of the recent info from the Science Journal - nothing new for the regular readers of the Science Journal, but I thought since David Baker is out of town and we have to do without his "inspiration" this week, some encouragement would be ok...
44) Message boards : Rosetta@home Science : Folding@home vs. Rosetta@home (Message 18454)
Posted 11 Jun 2006 by Profile Hoelder1in
Post:
See the thread What is the difference between all these protein related projects?, discussing exactly these things over the last couple of weeks. I don't think it makes sense to duplicate what was said there in this new thread.
45) Message boards : Rosetta@home Science : Rosetta@home Web Site Translations (Message 18253)
Posted 9 Jun 2006 by Profile Hoelder1in
Post:
As I don't know if administrators want to use my version or Hoelder1in version,
I've put my draft here
I'll continue to work on it next week, but feel free to improve/correct it

...well, I just wanted to make a suggestion, I have no intentions to provide a full en.po file myself. There are certainly different ways to do this... ;-)
46) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 18252)
Posted 9 Jun 2006 by Profile Hoelder1in
Post:
Since there has been a lengthy discussion in this thread, on whether "Folding@home's approach has become somewhat obsolete", here is my subjective, non-expert view on this:

At the time Folding@home started (I participated from shortly after the project was announced, I think in 98 or 99) there was a lot of talk about the Human Genome Project and how we would be able to read the letters of the genome but not understand their meaning. Computing the 3D structures of the proteins from their sequence that could be read off the genes seemed to be the most straight forward approach to tackle that problem, even from my laypersons point of view - and Folding@home seemed to be the only game in town where my humble computer (300 MHz PII at the time ;-) would be able to actually participate in and it felt great !

There were some nagging doubts, however, whether Folding@home's molecular dynamics approach would be really the most promising method to solve the "protein folding problem" (determining the 3D structure of proteins to atomic resolution by computational means) but I figured that as long as no one else seemed to be able to solve the problem by other, more efficient computational methods, Folding@home's work would perhaps at least lay the ground work for being able to solve the problem sometime down the line. Another thing that cast some doubt on Folding@home's work was when I learned that there was such a thing as CASP in which Folding@home didn't even participate.

So yes, if one thinks that Folding@home's eventual goal is to solve the "protein folding problem" as defined above, its approach seems somewhat peripheral (though perhaps useful for some questions, like mis-folding), and given the fact that there are now, since very recently, other approaches that, at least for a fraction of the smaller proteins, actually do solve the problem (as described in the Rosetta Science paper from October), perhaps also somewhat obsolete.

Well, just my personal take on this - and by the way: I am not the person who wrote that statement in Wikipedia. ;-)

Here are the only two statements by David Baker I found where he commented on Folding@home in the forum and I doubt he will ever say anything more specific that could be regarded as criticism of his colleagues' work: ;-)

26 Sep 2005
The Rosetta@home project goals are very different from those of Folding@home. The goal of Folding@home, I believe, is to determine how long proteins take to fold, given the sequence of the protein and knowledge of its three dimensional structure. The goal of Rosetta@home is to predict the three dimensional structure from the amino acid sequence. As explained in the Daily Telegraph article and the press releases, Rosetta has been the best method for structure prediction for quite some time...[i]

10 Dec 2005
[i]...Rosetta@home is very different from folding@home. rosetta@home aims to predict naturally ocurring protein structures and design new and useful ones; folding@home is simulating the process of protein folding.

47) Message boards : Rosetta@home Science : Rosetta@home Web Site Translations (Message 18168)
Posted 8 Jun 2006 by Profile Hoelder1in
Post:
Well, in the Seti .po file, they've done that, so I've done the same thing with the Rosetta draft.
Perhaps your method is better, I don't know...Let the administrators decide what's easier for them

See this example from SETI:

msgid "ACTIVATE_OR_CREATE"
msgstr "Special instructions: <ul><li> %s For SETI@home Classic participants %s "
"<li> %s For users of command-line, Mac Menubar, and pre-5.0 clients %s .</ul>"

or this one:

msgid "PART_REQ"
msgstr "<ul> "
"<li> There is an initial download of about 10 MB. "
"<li> You'll need about 20 MB of free disk space and 64 MB of RAM. "
"<li> with a typical computer (such as a 2 GHz Pentium 4), "
"you'll need to let SETI@home run for at least 2 hours per week "
"(slower computers are fine but they'll have to run proportionally more). "
"</ul> "

and I think David Kim also suggested to include the whole list in on msgstr.

-H.
48) Message boards : Rosetta@home Science : Rosetta@home Web Site Translations (Message 18163)
Posted 8 Jun 2006 by Profile Hoelder1in
Post:
Ok, I've looked a little at the Seti home page .po file.

If you want a underlined link you have to put a % sign : %your underlined link%
To do a black dot it's <ul><li>first</li><li>second</li></ul> like html

So for Rosetta it should be (I just give an exemple)

msgid "YOUR_ACCOUNT"
msgstr "<ul><li>%Your account% - view stats, modify preferences</li></ul>"

msgid "TEAMS"
msgstr "<ul><li>%Teams% - create or join a team</li></ul>"

There is a lot of <ul><li> </li></ul> tags IMHO: is there a more simple way to do black dots.
Can someone confirm before I modify the draft ?

Just had a look at the SETI en.po file: I think you need to write "%s" instead of just "%" to obtain a link. Also, I don't think it is necessary to have a separte msgid and msgstr for each line of text as in your example. You would save yourself and David K. a lot of work by placing whole blocks of text in one msgstr:

msgid "RETURNING_LIST"
msgstr "<ul><li>%sYour accound%s - view stats, modify preferences"
"<li>%sTeams%s - create or join team"
"<li>%sApplications%s"
"<li>%sServer Status%s"
"<li>%sAdd-ons%s</ul>"
49) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 18058)
Posted 8 Jun 2006 by Profile Hoelder1in
Post:
Here is how I described the differences between R@h and F@h from my point of view, as well as my (subjective) reasons to leave F@h for R@h, in another forum:

The two projects are indeed different. They have different goals and they use different methods:

While Folding@home wants to understand how proteins fold, by calculating the intermediate, partly folded states in sequence, Rosetta@home attempts to determine the endpoints of the folding process, i.e., the final 3-dimensional folded shapes of proteins, from their sequence of amino acids (the protein folding problem) - and by reversing this process, to determine amino acids sequences that fold into specific, pre-determined shapes (protein design).

So how does this relate to medical relevance (finding cures):

Since Folding@home studies the details of the folding process, this approach seems particularly suited to study mis-folding which is at the heart of some diseases, Alzheimer's comes to mind foremost. Another would be Mad Cow Disease, I am not sure there are many more others but my knowledge on this may be incomplete.
In the case of Rosetta@home I think it is obvious that the capability to design proteins with specific shapes and active sites that are able to perform specific functions in the body has immediate relevance for drug design. Rosetta's capability to determine the 3D shapes of proteins from their amino acid sequence on the other hand helps to determine the function those proteins perform in the body and to identify potential drug targets. See the Disease Related Research page at the Rosetta website and the statements by David Baker about "enzyme design" that I quoted in my previous post. Info on Alzheimer's/mis-folding related research at Rosetta is available here .


Perhaps I should also explain what got me to crunch for Rosetta: I originally participated in Folding@home for a number of years but decided to switch over to Rosetta, shortly after Rosetta went public, when Vijay Pande had spoken favorably of Rosetta and of David Baker's work on the Folding@home forum. Here are my reasons for the switch-over:

  • Rosetta at the time was (and still is) the much smaller project in terms of participants - so I felt my contribution would make more of a difference there and it also seemed to be sort of fair that both projects should have access to similar amounts of computing power. So in fact lots more Folding@home participants would have to switch over to Rosetta. ;-)
  • over the years I never really understood how the science done at Folding@home would eventually lead to treatments or cures. With Rosetta the connection to identifying drug targets and to drug design seemed much more obvious.
  • somewhat related to the last point, I never really understood the science behind Folding@home. I mean what is it that we really learn by following the folding path of a protein - I understand the intellectual challenge and fun of being able to do that, but what is the point ? With Rosetta it seemed much easier to understand what the project was after.
  • after participating in Rosetta for a while I also began to enjoy the direct contact to David Baker and the other team members. David Baker is very good at making everyone feel a part of the team and whenever I had a question about the project it was immediately answered. The project is also very willing to take up suggestions by team members.


I thought this might fit in with your discussion...

50) Message boards : Rosetta@home Science : A question about energy (Message 17921)
Posted 7 Jun 2006 by Profile Hoelder1in
Post:
...why is it negative at times? How can you have a negative energy?

You guys seem to be missing an important point. I don't know how the Rosetta energies are calculated in detail, but in general, a negative total energy is exactly what makes the atoms stick to each other to form a protein. The atoms are hold together by attractive electrostatic forces. Whenever you have an attractive force field the potential energy is negative. The condition for an atom to be bound to a protein is that its total energy (the sum of its positive kinetic and negative potential energy) is negative. If you increase the kinetic energy of the atoms by heating the protein, the atoms will wiggle around faster and faster till they break their chemical bonds and the protein is destroyed and this will happen exactly at the point when the kinetic energy becomes large enough to cancel out all of the negative potential energy.
51) Message boards : Rosetta@home Science : Rosetta AP article! (Message 17361)
Posted 30 May 2006 by Profile Hoelder1in
Post:
http://seattlepi.nwsource.com/local/6420AP_WA_Research_at_Home.html

So could it be that AP intended the article only for local consumption ? So far it only seems to have been carried by news media within the State of Washington (try a Google News search with 'Rosetta@home' and 'Donna' in the search window, for example).
52) Message boards : Number crunching : Report Problems with Rosetta Version 5.16 I (Message 16738)
Posted 21 May 2006 by Profile Hoelder1in
Post:
This result exited with code "1" giving the error message:

ERROR:: Exit at: dock_structure.cc line:401

This is a somewhat old Linux-box with just 256 MB memory but usually it runs stable - this is its first error in, I guess, months...
53) Message boards : Number crunching : Improvements to Rosetta@home based on user feedback (Message 16540)
Posted 18 May 2006 by Profile Hoelder1in
Post:
I did contact Akos a while ago, but he for the moment wants to focus on further improvements to the Einstein code.

See this New Scientist article on Akos' Einstein work. So maybe he now completed his Einstein code speed-up activities and is looking for new challenges... ;-)
54) Message boards : Rosetta@home Science : R@H Volunteer update: Tell-a-friend (Message 16202)
Posted 13 May 2006 by Profile Hoelder1in
Post:
I EMailed myself, and Yahoo! Mail dropped it right in the bulk mail (i.e. SPAM) bin. Is that due to making the reply to EMail not match the sender?

Same with me. It also ended up in the SPAM folder. Also, I usually have the "Do not load remote images in Mail & Newsgroup messages" option set in Mozilla. So the images were not displayed. The same happend with the recent "Letter to Rosetta@home crunchers". Perhaps the letter should be designed in such that it also makes sense without the images ? The fonts you used come out rather large, by the way. I can't believe that you intended them so large - perhaps IE displays them smaller ?
55) Message boards : Rosetta@home Science : Rosetta video/outreach project (Message 16166)
Posted 13 May 2006 by Profile Hoelder1in
Post:
p.s Yes, Jupiter is a gas giant, we have been planning on re-shooting David's analogy to say "a planet the size of jupiter" or "a large planet." Sorry, should have clarified that in the original post. Any suggestions on shorthand for "a large planet" that brings to mind an immediate mental picture besides "jupiter"?


Why not just use good old Earth as an example in the planet analogy?

Everest, Dead Sea. see Extremes on Earth

Yes, why not use the example from the "lecture" (death valley vs. dead sea). Rocky planets (the ones with a surface one can stand on) larger than Earth nowadays are called super-Earths, though I think it is not clear whether super-Earths the size of Jupiter are even possible. Due to the large gravity the height of mountains would at any rate be much smaller than on Earth.
56) Message boards : Rosetta@home Science : Rosetta video/outreach project (Message 16136)
Posted 13 May 2006 by Profile Hoelder1in
Post:
-David Baker- elevation analogy

I like the elevation analogy a lot - however, minor correction, Jupiter is a socalled "gas giant", and a such does not have a surface one can parachute down to. ;-) See here.
57) Message boards : Rosetta@home Science : Comments/questions on Rosetta@home journal (Message 15642)
Posted 7 May 2006 by Profile Hoelder1in
Post:
http://norfolk.cs.washington.edu/htbin-post/unrestricted/colloq/details.cgi?id=449

Absolutely worth watching.

I agree, and believe that you are your own worst critic (all of us are), and my focus on your presentation was on what you had to say. I found it fascinating, and a means to get to know you better. So David, I would suggest featuring the link on the project main page. Very worthwhile!

Indeed !

There is one specific question I wanted to ask, though: right at the end of the lecture there was a statement which seemed to say that the work about cutting DNA at specific sites (as described on the "Disease Related Research" page) was already under way. I would definitely be interested to hear how far this work has proceeded (e.g., in terms of developing this for therapeutic purposes) and what is planed for the future. Thanks, -H.
58) Message boards : Rosetta@home Science : Discussion- Proteins and Work Units (Message 15388)
Posted 3 May 2006 by Profile Hoelder1in
Post:
I would guess that the size of a small protein in its native state must be something like 50 atoms across, so the size of a protein would be a few Nanometers or more (I am not a bio science guy either, I am sure the experts will be able to give you more accurate numbers).

a little bigger, you have to take into account the size/length of the bonds

I was speaking of the diameter of the folded, native state of proteins, not the length of the chain. It seems eberndl's list confirms my crude estimate. :-; BTW: I am amazed how small some prokaryotes seem to be, just hundreds of small proteins across - it must be terribly cramped in there...
59) Message boards : Number crunching : Report Errors for Rosetta Version 5.06 (Message 14838)
Posted 28 Apr 2006 by Profile Hoelder1in
Post:
All my v5.06 WUs are failing with exit code 2 ! See here. I am away from my computer right now, so I can't tell you anything more than that (there were no problems with the v5.06 WUs that I crunched on Ralph).

UPDATE: All the ones sent before 7:46 UTC crashed immediately; this one seems to be doing ok so far.
60) Message boards : Rosetta@home Science : Discussion- Proteins and Work Units (Message 14748)
Posted 27 Apr 2006 by Profile Hoelder1in
Post:

I am not a bio science guy but, If I read this description of 1tul correctly, the reference to "Resolution" gives some idea of the size. I can't tell if this is the field size required for the thing to fit into to be resolved or the actual size of the protein itself.

As a rule of thumb the size of an atom is about 1 Angstrom; so if the resolution isn't much larger than 1 Angstrom this is close-to-atomic resolution and it can't get any better than that. I would guess that the size of a small protein in its native state must be something like 50 atoms across, so the size of a protein would be a few Nanometers or more (I am not a bio science guy either, I am sure the experts will be able to give you more accurate numbers).


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