I wanted to give you a very brief overview of the results so far and what will be coming next.

We have results now for nine proteins. For two of these (2reb and 1dtj) all of the lowest energy structures are extremely close to the correct structure. For most of the remaining proteins, there are one or two quirks which prevent the low rmsd structures from achieving very low energies (like a puzzle where the last piece won't fit). Our goal, of course, is to be able to compute the structures of all of these proteins as accurately as we can for 2reb and 1dtj. For remaining proteins, it is clear that if we cheat and guide the runs close to the correct structure, they fall into the energy minimum surrounding the native structure, but we just haven't been getting close enough in the unbiased runs (this is the "wall" that people have commented on). From analysis of the results thus far, we have made a number of improvements to the method, that from our limited in house tests suggest should significantly improve the results on all the proteins.

You will be seeing two new things in the next several weeks. First, I will be testing the improvements mentioned above systematically on a set of eleven proteins to get a clear idea of how effective each improvement is individually, and to see what challenges still remain. Second, you will start seeing jobs submitted by some of the very talented other scientists in our research group. David Kim is just developing an internal queuing system that will make the BOINC resource available to other group members (up to now I've been rather unfairly monopolizing it!). Each scientist will be posting explanations of what they are doing and what they are learning. Also, David will get to start using BOINC for his own scientific research--he has had time for nothing but building the infrastructure to support the project for the past several months, but with more people in the group contributing and much in place already he will very deservedly get to use this terrific resource for his research on structure prediction.

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Thanks for the update.....much appreciated!


Cheers and looking forward to crunching the dieseas calculations

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I forgot to mention that we think we have found a possible contributor to the "stuck at 1%" problem. In the next few days we will be sending out a new version of the code with this problem fixed and some additional new features we would like to test.

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well hope that you found it.. i certanly am hopefull

and ohh did someone say new features... ohh cant wait... can we get a peak at what they are...

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A big thanks for this status update David. These messages encourages users to keep crunching at full speed, and surely can attract new users to the project.
I hope we can read such messages more in the future.

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Member of Dutch Power Cows

I wanted to give you a very brief overview of the results so far and what will be coming next.

We have results now for nine proteins. For two of these (2reb and 1dtj) all of the lowest energy structures are extremely close to the correct structure. For most of the remaining proteins, there are one or two quirks which prevent the low rmsd structures from achieving very low energies (like a puzzle where the last piece won't fit). ... but we just haven't been getting close enough in the unbiased runs (this is the "wall" that people have commented on). From analysis of the results thus far, we have made a number of improvements to the method, that from our limited in house tests suggest should significantly improve the results on all the proteins.

...

I don't know if you read my post towards the bottom of this thread, if not, you may have some mind reading ability. :)

This is exactly the sort of information that keeps me glued to a project, because it tells me what is going on with all the crunching I'm doing.

That being said, the one question that comes to mind, and it's been a concern of several of us. When you refer to the "wall", is that what creates the effect we see on the best prediction graphs where it looks like there's a bounding line around the lower and left sides of the cluster?

Also, in the "breakthrough" thread, you mentioned that you'd had an idea that tried to make the map a bit more "sloped". Is this related to the wall, and the improvements that you have tested in house and will be releasing soon?

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I wanted to give you a very brief overview of the results so far and what will be coming next.

We have results now for nine proteins. For two of these (2reb and 1dtj) all of the lowest energy structures are extremely close to the correct structure. For most of the remaining proteins, there are one or two quirks which prevent the low rmsd structures from achieving very low energies (like a puzzle where the last piece won't fit). ... but we just haven't been getting close enough in the unbiased runs (this is the "wall" that people have commented on). From analysis of the results thus far, we have made a number of improvements to the method, that from our limited in house tests suggest should significantly improve the results on all the proteins.

...

I don't know if you read my post towards the bottom of this thread, if not, you may have some mind reading ability. :)

This is exactly the sort of information that keeps me glued to a project, because it tells me what is going on with all the crunching I'm doing.

That being said, the one question that comes to mind, and it's been a concern of several of us. When you refer to the "wall", is that what creates the effect we see on the best prediction graphs where it looks like there's a bounding line around the lower and left sides of the cluster?



yes, this is what I was referring to. for two of the proteins we are clearly breaking through, and from an in house test I just looked at it looks like this might be happening for a third (1ogw) as well. I'm optimistic the tests coming up will show how to solve the problem for more of the proteins



Also, in the "breakthrough" thread, you mentioned that you'd had an idea that tried to make the map a bit more "sloped". Is this related to the wall, and the improvements that you have tested in house and will be releasing soon?

yes. the breakthrough idea was a way to let the protein have more freedom, so it can wind its way through narrow channels on the landscape. but the results from the last several weeks have shown quite clearly that I went too far in giving the chain more freedom--searching improved, but with the new freedom the chain wandered into regions that would normally be forbidden (you can see these as low energy regions distant from the true structure; 1ogw was a clear case of this). the next batch of runs I think will have just the right amount of additional freedom--enough to improve the search without trapping in physically unrealistic energy minima.

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Thanks for the update, appreaciated.

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...
This is exactly the sort of information that keeps me glued to a project
...

and that attracted me to your project just this week - I'm more of a physicist than a bio but I like the level of explanation you guys are giving

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This is exactly the sort of information that keeps me glued to a project, because it tells me what is going on with all the crunching I'm doing.

I second that!



I was also wondering if the 'Results' and 'Top predictions' pages will be updated for the New Year?

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This is exactly the sort of information that keeps me glued to a project, because it tells me what is going on with all the crunching I'm doing.

I second that!

I find that a project gets "stale" without some kind of regular input from the project scientists. I guess I feel that if they don't believe their project is worth some of their attention on a regular basis, perhaps my contribution is not worth it on a regular basis!

So, again, kudos to R@H, who I know really appreciates my contribution! :)

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Regards,
Bob P.

Thanks for the info David. This indeed is exactly the info we users want. Know what we're doing. Keep that up :)

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Proud member of the Dutch Power Cows

This is exactly the sort of information that keeps me glued to a project, because it tells me what is going on with all the crunching I'm doing.

I second that!

I find that a project gets "stale" without some kind of regular input from the project scientists. I guess I feel that if they don't believe their project is worth some of their attention on a regular basis, perhaps my contribution is not worth it on a regular basis!

So, again, kudos to R@H, who I know really appreciates my contribution! :)

HI Bob, I feel just the same way. If we can't explain to you what we are doing and what the results of the last few weeks are, we don't deserve your help! David

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yes i am very pleased with the support and such you have all givein back to us when we asked.

the one question i have is how often will you update the results page
(alot of us got spoiled by FaD)

2005-11-16 1hz6A_abrelaxmode_random
2005-11-15 1acf__abrelax
2005-11-15 1acf__abrelax_no_cst
2005-11-15 1bmbA_abrelax
2005-11-15 1bmbA_abrelax_no_cst
2005-11-15 1btn__abrelax
2005-11-15 1btn__abrelax_no_cst
2005-11-15 1cfyA_abrelax
2005-11-15 1cfyA_abrelax_no_cst
2005-11-15 1pvaA_abrelax
2005-11-15 1pvaA_abrelax_no_cst


if i am reading this correctly the last update to the results we can view is the 16th of last month. being that i am on a very limited bandwith at this time (ship at sea) i dont want to try to download something large and find out there has been no update.. am i reading it right that 11/16 is last update..

i am definatly pleased at the project here and from what i can see.. curently i have my computers running to produce about 50-60% total from 4 computers to this project and if you look at the stats below you can see that i do look at every project i can and decide as i have time what to do and how much

your updates and informatin you are giving us is makeing me happy and feel to me that its worth leting my computers run while i am at sea verses turning them off to save power.

keep up the good work (oh and any hints on whats comming next??? or new features?)

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this is so exciting, great job!!!!

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yes i am very pleased with the support and such you have all givein back to us when we asked.

the one question i have is how often will you update the results page
(alot of us got spoiled by FaD)

2005-11-16 1hz6A_abrelaxmode_random
2005-11-15 1acf__abrelax
2005-11-15 1acf__abrelax_no_cst
2005-11-15 1bmbA_abrelax
2005-11-15 1bmbA_abrelax_no_cst
2005-11-15 1btn__abrelax
2005-11-15 1btn__abrelax_no_cst
2005-11-15 1cfyA_abrelax
2005-11-15 1cfyA_abrelax_no_cst
2005-11-15 1pvaA_abrelax
2005-11-15 1pvaA_abrelax_no_cst


if i am reading this correctly the last update to the results we can view is the 16th of last month. being that i am on a very limited bandwith at this time (ship at sea) i dont want to try to download something large and find out there has been no update.. am i reading it right that 11/16 is last update..

i am definatly pleased at the project here and from what i can see.. curently i have my computers running to produce about 50-60% total from 4 computers to this project and if you look at the stats below you can see that i do look at every project i can and decide as i have time what to do and how much

your updates and informatin you are giving us is makeing me happy and feel to me that its worth leting my computers run while i am at sea verses turning them off to save power.

keep up the good work (oh and any hints on whats comming next??? or new features?)

I apologize for the delay in updating the results page--we are doing a lot of behind the scenes work to enable multiple scientists in my group to access this amazing computing resource. Everybody using the resource will share the responsibilities of reporting our results back to you, and so you will see much more frequent updating of results and other feedback in the new year.

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I apologize for the delay in updating the results page--we are doing a lot of behind the scenes work to enable multiple scientists in my group to access this amazing computing resource. Everybody using the resource will share the responsibilities of reporting our results back to you, and so you will see much more frequent updating of results and other feedback in the new year.

So will each scientist that uses R@H be a R@H member and provide feedback on the message boards? (I know there's already Ppoject scientists already active on the boards.)

I was thinking that if scientist X submits work and we have questions about X's submitted work, will X be available on the message boards to answer questions? Will you make it mandatory to each scientist to be available on the message boards in case there's specific questions/concerns about their work (or if they don't update their own result pages :P)?

Or in a word... accountability :)

I'm only asking because R@H has great communication from its project devs, and scientist and I'd like to see that continue when you let more scientists use R@H.

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Another voice in the chorus...

Thank you David (and Rosetta@Home et.al.)

Sometimes I understand what you (all of you) discuss and others I don't, but none the less, it is such a pleasure to feel this connected to what my computers are doing.

Our TeAm at Anandtech continues to grow and the excitement is far above that which would be the norm for a new project (we all love new projects). It is because of your (all of you) entheusiasm and wilingness to make us part of it all.

I am anxious to see new behaviors of my PCs as they work and then take a trip to this great forum to find out what it all means!

KUDOS

-Sid

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Proudly crunching with TeAm Anandtech

I apologize for the delay in updating the results page--we are doing a lot of behind the scenes work to enable multiple scientists in my group to access this amazing computing resource. Everybody using the resource will share the responsibilities of reporting our results back to you, and so you will see much more frequent updating of results and other feedback in the new year.

So will each scientist that uses R@H be a R@H member and provide feedback on the message boards? (I know there's already Ppoject scientists already active on the boards.)

I was thinking that if scientist X submits work and we have questions about X's submitted work, will X be available on the message boards to answer questions? Will you make it mandatory to each scientist to be available on the message boards in case there's specific questions/concerns about their work (or if they don't update their own result pages :P)?

Or in a word... accountability :)

I'm only asking because R@H has great communication from its project devs, and scientist and I'd like to see that continue when you let more scientists use R@H.

yes, that is the plan. also, we will be able to divide up the other tasks, such as posting updated results on the site, etc.

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yes, that is the plan. also, we will be able to divide up the other tasks, such as posting updated results on the site, etc.

Thanks for replying on the last Saturday before Christmas!!!

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