Discovering Dengue Drugs-together
http://www.utmb.edu/discoveringdenguedrugs-together/Main Page.htm

New Approaches to Structure-Based Discovery of Dengue ProteaseInhibitors

HELP CURE MUSCULAR DYSTROPHY

http://www.ihes.fr/~carbone/HCMDproject.htm

Phase I, with cross-docking of 168 proteins, has been completed.
Phase II, with targeted cross-docking of about 2200 human proteins whose three dimensional structures are known (and stored in the Protein Data Bank www.rcsb.org/pdb) will be launched at the end of march-beginning april 2009. The set of proteins include those found to be mutated in neuromuscular disord


Publications
S. Sacquin-Mora, A. Carbone and R. Lavery (2008), Identification of protein interaction partners and protein-protein interaction sites, J. Mol. Biol. 382, p1276-1289.


S. Engelen, L.A. Trojan, S. Sacquin-Mora, R. Lavery and A. Carbone (2009), Joint Evolutionary Trees: a large scale method to predict protein interfaces based on sequence sampling, PLoS Comp. Biol. 5(1): e1000267. doi:10.1371/journal.pcbi.1000267.

 

Nutrious Rice For the World

http://protinfo.compbio.washington.edu/rice/video.html


The goal of this website is to provide information about proteins. It is dedicated to the application of methodologies developed by our group on proteins that are of particular interest to the scientific community. Thus this serves as a complement to our Bioverse database and webserver and other resources available as a result of our computational biology activities (see credits).

http://protinfo.compbio.washington.edu/


Help Conquer Cancer

Technical launch date: November 1, 2007;

Official launch date: November 5, 2007.

• January 2008 update
• May 2008 update
• October 2008 update
• April 2009 update
• October 2009 update
• March 2010 update

             Since the launch of HCC project in November 2007, WCG members contributed over 46,906 years of run time, averaging over 53 years of computation per day. To date 64,724,807 results were returned (Statistics Last Updated: 3/26/10 00:05:59 (UTC)).

             Using 12,375 primary features computed by the HCC project are augmented by a set of 2,533 features computed from the primary, creating a final set of 14,908 features. These image features and a massive training set of 165,351 hand-scored images were used to train multiple Random Forest classifiers that accurately recognize multiple crystallization outcomes, including crystals, clear drops, precipitate, and others. The system successfully recognizes 80% of crystal-bearing images and 95% of clear drops. Some of these results have recently been summarized and published in the Journal of Structural and Functional Genomics: Cumbaa, C. A. and Jurisica, I. Protein crystallization analysis on the World Community Grid, J Struct Funct Genomics, 11(2): R13, 2010.

            We are happy to announce a significant performance improvements to the Help Conquer Cancer project. Resulting from a collaboration with the IBM Toronto Software Lab, the optimized HCC software will process work units in less than half the time.

Further details about the March 2010 update

The Human Proteome Folding Project

• Public Data Repository: results from the Human Proteome Folding Project can be found here (associated with the Yeast Resource Center).

Fight AIDS@Home

Fight AIDS@Home Newsletter Volume 8: Nov 2, 2009 pdf

The FightAIDS@Home Project uses the volunteered computing power of the World Community
Grid to test candidate compounds against the variations (or “mutants”) of HIV that can arise and
cause drug resistance. FightAIDS@Home recently identified several fragments as new
candidates for a novel binding site on the peripheral surface of HIV protease. These fragments
docked well against the “exo site,” and our collaborators recently began in vitro studies (i.e.,
“wet lab” experiments in test tubes) to assess their potencies. If these wet lab experiments
produce promising results, then these fragments could form the foundation for the development
of “allosteric inhibitors” of HIV protease (i.e ., “flexibility wedges” that can disrupt the
conformational changes that HIV protease must undergo in order to function). These allosteric
inhibitors could represent a totally new class of anti-AIDS compounds. READ MORE

http://fightaidsathome.scripps.edu/status

Two Compounds Discovered that Pave the Way for New Class of AIDS Drug

IBM World Community Grid’s Computing Strength Powers Breakthrough Research that will Guide their Development

GPUGrid.net

http://multiscalelab.org/gianni/publications

High-throughput all-atom molecular dynamics
simulations using distributed computing
I. Buch,† M. J. Harvey,‡ T. Giorgino,† D. P. Anderson,¶ and G. De Fabritiis∗,†


Folding at Home

Results:
Here are the peer reviewed results from Folding@home. We stress that it can take quite a while to go from a result to a published peer review article (often as much as a year). Also, these articles are written for fellow scientists, so they are fairly technical. However, these papers represent our progress to date that's publicly available, with lots more on the way.

http://folding.stanford.edu/English/Papers

January 17, 2010

Paper #72: Major new result from Folding@home: simulation of the millisecond timescale

 Simulating protein folding on the millisecond timescale has been a major challenge for many years.  When we started Folding@home, our first goal was to break the microsecond barrier.  This barrier is 1000x fold harder and represents a major step forward in molecular simulation.

Specifically, in a recent paper (http://pubs.acs.org/doi/abs/10.1021/ja9090353), Folding@home researchers Vincent Voelz, Greg Bowman, Kyle Beauchamp, and Vijay Pande have broken this barrier. The movie below is of one of the trajectories that folded (i.e. started unfolded and ended up in the folded state). From simulations like these, we have found some new surprises in how proteins fold. Please see the paper (url above) for more details.

Why is this important?  This is important since protein misfolding occurs on long timescales and this first simulation on the millisecond simulation for protein folding means we have demonstrated our new Markov State Model (MSM) technology can successfully simulate very long timescales.  It make sense to go after protein folding first, since there is a wealth of experimental data for us to test our simulations. 

While this paper on protein folding has just come out, we have already been using this MSM technology to study protein misfolding in Alzheimer's Disease, following up from our 2008 paper. While our previous paper was able to get to long enough timescales to see small molecular weight oligomers, this new methodology gives us hope to push further with our simulations of Alzheimer's, making more direct connections to larger, more complex Abeta oligomers than we were previously able to do.

Publications:

A complete list of all papers from the group is given below. Papers from Folding@home related work are also available, with abstracts, lay summaries, and PDF downloads on the Folding@home papers page.

Also, check out the PubMed Summary and Google Scholar Summary (ordered by citation count).

Thank you to the members of World Community Grid!

 The research team at Chiba Cancer Center would like to thank World Community Grid members for their valuable CPU time contributions to the Help Fight Childhood Cancer project. Because of your generous support, World Community Grid has processed the first three drug targets faster than expected. The preliminary results look very promising and we will provide more information about this at a later time. In the meantime, we have identified two other drug targets that we would like to process on World Community Grid and should have this work unit data ready in about 2 months or earlier. Again, thank you for your all of your help. We are pleasantly surprised at how World Community Grid has so rapidly advanced our research on curing childhood neuroblastoma cancer.

Thank you,
Dr. Akira Nakagawara

June 27, 2010

With Folding@home (FAH), we have the computer power to tackle challenging problems involved with protein folding.  One of the interesting folding-related problems has to do with how proteins (and their conformational change) catalyze viral infection.  While viral infection is not a major thrust of FAH, it has been a pilot project for several years.  

We are happy to announce the publication of some of our recent FAH scientific results:
"Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails"
This work represents a major step forward in this project, as we can now study the process in all-atom detail and get some better sense of the role of proteins and protein conformational change in the process.

This paper describes work on the mechanism of vesicle fusion, a process involved in viral infection, the transmission of nerve impulses, and cellular secretion.  In it, we have analyzed the mechanism of membrane fusion in greater detail than previously feasible, yielding predictions for how influenza may use this mechanism to enter cells.  This analysis was powered by our Folding@Home donors.  FAH project 2681 directly contributed to this work; we are also following up several other avenues.

 Graphics, links and summary at F@H