The Lilypad Register no. 53 (April, 16 2004)

[BuiesCreek847]

Folks, I'd like to welcome you to the 53rd edition of "The Lilypad Register", a once a week or so newsletter devoted to the AMDmb.com Folding Frogs. Here, you will find listings of our Team members milestones attained, notices and links to new members threads, as well as notices and links to mick 100 (Link) and Justin500 (Link) award threads. When appropriate, we'll post important info from Stanford. If you, the Team members, become aware of news worthy events, please PM BuiesCreek847 (David), or kiddetoolman (Tommy) so that we may post it here.

Here's the Owners Manual (Link) for it.



* The Genome@Home project's done.

The Genome@home servers have now been shut down. The project will officially end with the final stats update this morning. The project website will be updated to reflect the end of the project.

Thank you all for everything you've done to make this project such a success. I encourage you all to continue donating your computer time to scientific research through the Folding@home project.

All the best - Stefan Larson

* Folding Fact of the Day

We have added a new "Fact of the day" to the stats (Stanfords). These were gathered by Tug Sezen, our resident high school teacher, in order to try to "spice things up" a bit. As the name implies, these facts change every day.

Hope you find it interesting.
Vijay

* Did you know?

Tug has updated his education pages and we've (finally) put them up. There is updated info on G@H, lay explanations of some of our important papers, and more! Actually, lots of neat stuff to explore. Don't miss the trivia game!

http://www.stanford.edu/group/pandeg...ing/education/

Vijay

* We lost a fine Folding Moderator

UpAllNight (Steve) has had to step down as one of our Folding forum moderators so as to focus on family matters during his fathers illness.

Steve started his Moding career here on 06-14-2003. He's been the backbone of the AAFx project since its inception as well as the welcome ambasador for new members.
Doing a search for his posts in the Folding forum exclusively, I find a minimum of over 1000! Truly a great contributor.

We're gonna miss him and hope he can stop in sometime.

You can wish him well in a thread Tommy started; A heart felt Pat on the Back to UpAllNight (Link)



* In an effort to serve you better,

Ryan (Owner of amdmb.com/pcperspective.com) has just upgraded some hardware in the forum server. It's gone from dual Athlon MP 1.2 GHz CPUs to dual Athlon MP 2800+ CPUs and 2 GB of DDR333 RAM. Kewl!

[BuiesCreek847]

Please Welcome our newest members in the past 7 days or so;
Be sure to welcome these fine folks.

• Hockster
• expense
• sturm375

Members earning the Justin500 (Link) award (500 Folding Points)

• rocket-ronnie (Link)
• Tigger0944 (Link)
• major_blunts (Link)
• DTKAEJOHNS (Link)
• Adopt-a-Frog_5 (Link)

Members earning the mick100 (Link) award (1,000 Folding Points)

• fruitloops (Link)
• rickikaye69 (Link)
• Tstorm (Link)
• Goofus (Link)
• DTKAEJOHNS (Link)
• Adopt-a-Frog_5 (Link)
• carlls (Link)
• jimzinsocal (Link)
• XC_Skier_Freak (Link)
• gfrag88 (Link)
• bigdoof (Link)
• troycanadian (Link)
• dwb (Link)

Members reaching new milestones; (Please post your congrats to these good folks here in this thread, thanks)
(This snapshot was taken at 11:20pm EST)



100 Folding Points

• David
• Alfer
• Mabmoro_Deventio

200 Folding Points

• Ky650

300 Folding Points

• Draciux
• xaeniac
• ohnl/;

400 Folding Points

• sirokket16
• dmdb
• Gatotsu
• Tony
• Lundgree
• Hockster

600 Folding Points

• major_blunts

700 Folding Points

• l3R3TT

1,100 Folding Points

• Tstorm
• carlls

1,200 Folding Points

• rickikaye69

1,300 Folding Points

• XC_Skier_Freak
• gfrag88
• fruitloops

1,400 Folding Points

• troycanadian
• bigdoof

1,500 Folding Points

• Steve612
• dwb

2,000 Folding Points

• buraianto
• Graphite

3,000 Folding Points

• titansfan098
• EtherGhost

5,000 Folding Points

• Andrew_RT
• greenmtns

6,000 Folding Points

• dancinbr

7,000 Folding Points

• Craigwd_2000
• freezepc

8,000 Folding Points

• Gatecrasher

9,000 Folding Points

• woodp

10,000 Folding Points

• dichead

11,000 Folding Points

• timread
• scuzzlebutt

12,000 Folding Points

• Zopilote

13,000 Folding Points

• Daniel_C_Irwin
• ChristianTrader

25,000 Folding Points

• Captain6Crunch

35,000 Folding Points

• Tbird761

40,000 Folding Points

• Inyourface1650

45,000 Folding Points

• SlimPickens
• BobH

50,000 Folding Points

• SENster7

60,000 Folding Points

• wscottcross

70,000 Folding Points

• Senor_Panadero
• NiNi

105,000 Folding Points

• Idahopackersfan2

120,000 Folding Points

• Coda

145,000 Folding Points

• lessell

245,000 Folding Points

• Sick_Willie

280,000 Folding Points

• BuiesCreek847

295,000 Folding Points

• UpAllNight

355,000 Folding Points

• Eldest_One

435,000 Folding Points

• Forg_Species_734

**If we've missed anyone, PLEASE let us know via PM. NOTE; Keep in mind, we've got to draw a line as to a cut off time for this newsletter, so don't think we're gonna miss you if you've reached a milestone recently (like in the last day or so).

Lets give a big hand to those who've worked so hard to reach these milestones. Their contribution to the Team and the F@H project is very much appreciated. Here's hoping you reach the next just as fast.


The Lilypad Register no.52 (April 7, 2004) (Link)
The Lilypad Register no. 51(Mar. 16, 2004) (Link)

[BuiesCreek847]

Team Name; Amdmb.com Folding Team
Team Rank; 10
Total Points; 9,293,043
Total WUs; 434,491
Users (Active); 1,014 (246)
(This snapshot was taken at 10:30pm EST)


Last 7 Days Production:

   Day   TotalPoints  WUs
04.16.04    22,205    530 
04.15.04    23,813    629 
04.14.04    29,610    646 
04.13.04    21,199    469 
04.12.04    22,627    609 
04.11.04    23,544    750 
04.10.04    21,279    596 
04.09.04    21,551    678

Tha AMDmb.com Folding Frogs stats

• As presented by Stanford (Link)
• As presented by coolrunr Stats for Amdmb.com Folding Frogs (link) ~Under Construction~
  
• Team overview as presented by extremeoverclocking.com (Link)
• Team overview as presented by foldingatwork.com (Link)
  
• Team members as presented by Statsman (Link)
• Team member details as presented by extremeoverclocking.com (Link)
  
• Forg_Species_734's stats (Link)

Team hosted Folding rig stats;

• Adopt-A-Frog_1's stats (Link) Hosted by Airmanv.
• Adopt-A-Frog_2's stats (Link) Hosted by wb22rules.
• Adopt-A-Frog_3's stats (Link) Hosted by kiddetoolman.
• Adopt-A-Frog_4's stats (Link) Hosted by hstroud.
• Adopt-A-Frog_5's stats (Link) Hosted by Superducky55.
• Adopt-A-Frog_6's stats (Link) Hosted by Dr. HaVoK. Coming soon to a monitor near you!
• Adopt-A-Frog_7's stats (Link) Hosted by ?. Currently soliciting a host!

Adopt-A-Frog host rules (Link)
Adopt-A-Frog Inventory (Link)

[BuiesCreek847]

Oohhh! The PandaGroup's got two newly released papers as of March 24th!

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy (link to pdf.file)
Christopher D. Snow, Linlin Qiu, Deguo Du, Feng Gai, Stephen J. Hagen, & Vijay S Pande. PNAS (2004)

ABSTRACT: We studied the microsecond folding dynamics of three hairpins (Trp zippers 1–3, TZ1–TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1–TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.

Does Native State Topology Determine the RNA Folding Mechanism?

(link to pdf.file)
Eric J. Sorin, Bradley J. Nakatani, Young Min Rhee, Guha Jayachandran, V Vishal, & Vijay S Pande. Journal of Molecular Biology (2004)

ABSTRACT: Recent studies in protein folding suggest that native state topology plays a dominant role in determining the folding mechanism, yet an analogous statement has not been made for RNA, most likely due to the strong coupling between the ionic environment and conformational energetics that make RNA folding more complex than protein folding. Applying a distributed computing architecture to sample nearly 5000 complete tRNA folding events using a minimalist, atomistic model, we have characterized the role of native topology in tRNA folding dynamics: the simulated bulk folding behavior predicts well the experimentally observed folding mechanism. In contrast, single-molecule folding events display multiple discrete folding transitions and compose a largely diverse, heterogeneous dynamic ensemble. This both supports an emerging view of heterogeneous folding dynamics at the microscopic level and highlights the need for single-molecule experiments and both single-molecule and bulk simulations in interpreting bulk experimental measurements.

Get your Free Adobie Acrobat reader HERE (link)

[BuiesCreek847]

It's time for me to update the stats links so bear with me.

Amdmb.com Related

Our very own Folding promotional video; Folding For Our Future (Link)

AMDmb website Welcome to The Pond

Our homepage Amdmb.com Folding Frogs!



Stanford Related

Stanfords HOME PAGE

Stanfords latest F@H client DOWNLOAD PAGE

Stanfords F@H CURRENT PROJECTS page

Stanfords F@H & G@H SERVER STATUS page

Tinker & GROMACS index of downloadable CORES (Win32, F@H & G@H)

Tinker & GROMACS index of downloadable CORES (Linux, F@H & G@H)

F@H client version HISTORY PAGE



F@H Client Installation
** We're Team no. 734 **


Folding Frogs First timers Folding@Home Set-up Guide (Link) as presented by kiddetoolman


Folding@Home advanced user Console Set Up Guide (Link) as presented by kiddetoolman



Windows 95/98/ME/NT/2000/XP Graphical client & Windows NT/2000/XP Screensaver Only client as presented by Stanford

Linux console (Linux/Intel) as presented by Stanford

READ and Understand the Folding@home Beta Testing F.A.Q. BEFORE downloading! Ask how to join the Beta Team in the Folding-community.org forum (Link below)
Index of publicly downloadable BETA beta (Win32 & Linux)
Beta client History.


*** Here's a neat, easy set-up program to run F@H as a service, written by coolrunr. Download it HERE (Windows) (Link) Or HERE (Linux) (Link) Be sure to check for any install notes HERE (Link)

*** Here's a list of current SWITCHES for use with each client.

Folding-Community.org

HOME PAGE



Other Helpful Links

Homesite of Electron Microscope III, F@H monitoring and other related software.

Website of FoldBorg Team statistics monitoring and related software as presented by Team Picard

[clawhammer]

wonderful job, as always. and excellent link, we've come a long way!

[BuiesCreek847]

Originally posted by clawhammer on 04-17-2004 at 12:17 AM
wonderful job, as always. and excellent link, we've come a long way!

Thanks Dude!

Gimme a bit to post the main pages news.

Then there's the minor detail of the awards.

[pimp my ride]

Originally posted by BuiesCreek847 on 04-17-2004 at 12:19 AM
Thanks Dude!

Gimme a bit to post the main pages news.

Then there's the minor detail of the awards.

Wait, this issue is from a month ago

[BuiesCreek847]

Originally posted by victimizati0n on 04-17-2004 at 12:25 AM
Wait, this issue is from a month ago

Having a "Calgon" day there Shawn?

Nah, I've been slack the last month and took some much needed time off. Steve was good enough to fill in for me with an issue last week.

[kiddetoolman]

Originally posted by BuiesCreek847 on 04-17-2004 at 12:28 AM
Having a "Calgon" day there Shawn?

Nah, I've been slack the last month and took some much needed time off. Steve was good enough to fill in for me with an issue last week.

*ah hem**



Good to have you back behind the madness of the Register.

[pimp my ride]

Well, another Great issue, thanks

[BuiesCreek847]

Out with the old and in with the new.