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What is the difference between the Vina and AutoDock software packages used in the FightAIDS@Home project?

AutoDock and Vina are automated docking software tools. They are designed to predict how a small molecule, such as a substrate or drug candidate, binds to a receptor molecule of known 3D structure. In the context of this project, these docking tools are being used to find potential drug compounds which may inhibit the HIV-1 protease (a protein which encourages and controls the progression of the virus).

The two software programs use different algorithms, each of which may provide better results depending on the types of molecules being docked. The FightAIDS@Home project uses both software tools in its calculations: the Scripps researchers determine ahead of time which software package is more suited to the particular task at hand, and the selected software for those work units then runs on World Community Grid. The project may therefore switch back and forth between the two software packages depending on its needs. As a contributor to the FightAIDS@Home project, you may notice either of those software packages being run for this project, each of which has a unique screen saver (see below for details on both screen savers).

What's new about Phase 2 of the FightAIDS@Home project? What will this phase of the project do?

Phase 2 of the project takes results from the molecular docking approach used in Phase 1 and produces a re-evaluation of the top hits found from the virtual screening, to further narrow down potential drug candidates.

While Phase 1 conducted virtual screening of chemical libraries using AutoDock and AutoDock Vina software tools, Phase 2 introduces a completely new computational method into the FightAIDS@Home effort: the BEDAM technique, implemented with Academic IMPACT software, a molecular simulation tool. Academic IMPACT models the thermodynamics of binding of a ligand to a protein including the reorganizational free energy of the docked complex. Much more computer time is needed to evaluate each docked complex, so only the top candidates from Phase 1's virtual screen are examined in this way.

How does the GO Fight Against Malaria software work?

The GO Fight Against Malaria project uses software that automatically downloads small amounts of input data and then performs calculations that model how well different drug candidates interact with various molecular targets from the malaria parasite. After your device finishes one set of calculations, the results are sent by World Community Grid to a computer at The Scripps Research Institute. The Scripps research team then analyzes the results produced by all of the different donor machines on World Community Grid.

This project uses AutoDock 4.2 and the new AutoDock Vina computer software to evaluate how well each candidate compound (molecule) attaches ("docks" or "binds") against a malarial target (usually a protein molecule.) Millions of candidate compounds will be tested against 14 different molecular drug targets from the malaria parasite in order to discover new compounds that can block (inhibit) the activity of these multi-drug-resistant mutant superbugs. These candidates will be tested by docking flexible models of them against 3-D, atomic-scale models of different protein drug targets from the malaria parasite, to predict (a) how tightly these compounds might be able to bind, (b) where these compounds prefer to bind on the molecular target, and (c) what specific interactions are formed between the candidate and the drug target. In other words, these calculations will be used to predict the affinity/potency of the compound, the location where it binds on the protein molecule, and the mode it uses to potentially disable the target. Compounds that can bind tightly to the right regions of particular proteins from the malaria parasite have the potential to “gum up” the parasite’s machinery and, thus, help advance the discovery of new types of drugs to cure malaria.

What are AutoDock 4.2 and AutoDock Vina?

These are two different types of “docking” programs, which allow us to computationally search for new compounds that might be able to bind to and block the activity of molecular drug targets from the malaria parasite. Both of these docking programs were created and developed by the Olson lab at The Scripps Research Institute (http://mgl.scripps.edu).

How do these docking programs work?

AutoDock is a suite of automated docking tools designed to predict how “small molecule compounds,” such as substrates or drug candidates, bind to a receptor (target) of known 3-D structure and to estimate how tightly that small molecule binds to that receptor. That is, it predicts both the small molecules “binding mode” and estimates its potency against the target. The AutoDock algorithm is essentially a high dimensional stochastic search utilizing a “Lamarckian genetic algorithm” approach with flexible models of the small molecules. When docking any given drug candidate against a particular protein target, the space of all possible configurations must be explored to find the best energetic fit between the two molecules. Any given docking protocol must explore all possible degrees of freedom that are specified in the system. AutoDock consists of two main programs: autodock performs the docking of each compound against a set of grid maps that describe the energetic landscape of the target protein, and autogrid pre-calculates these grid maps before autodock is run, which greatly increases the speed of the autodock phase of these calculations.

AutoDock Vina also uses pre-calculated grid maps (which are generated internally, instead of using a separate program, such as autogrid). Vina also uses flexible models of the small molecules, and it also treats the docking process as a stochastic global optimization of the scoring function. But Vina utilizes a different scoring function and a different search algorithm than AutoDock, and Vina’s search process is guided by the gradients in the energetic landscape of the target protein (unlike AutoDock4.2).

What is BEDAM and how has it been used in the past?

BEDAM stands for “Binding Energy Distribution Analysis Method”. It is a method developed by the Levy group which uses advanced sampling and analysis techniques to calculate absolute binding free energies based on a foundation in statistical mechanics and data generated from molecular dynamics simulations.

In a collaboration between the Olson group at The Scripps Research Institute and the Levy group at Temple University, BEDAM techniques were recently developed and used in a computational challenge (SAMPL4) demonstrating that docking coupled with subsequent BEDAM processing gives more reliable hits. This challenge used blind data from a pharmaceutical company working on HIV Integrase inhibitors. The AutoDock Vina/BEDAM modeling performed the best among all automated computational predictions submitted in the challenge.

When will this project be completed?

The first phase of the project ran through July, 2008.

Will there be a badge for GPU participation?

No. Your contributions using your GPU will contribute to a specific research project and count towards earning a badge for that project.

How often do research projects provide updates for volunteers?

Active projects: We ask the research team for each project to provide at least two formal updates per year. We also try to provide short monthly updates in the forum thread for each project.

Completed projects: We provide updates when completed projects publish papers, start or finish major experiments, or have other big news.

Why hasn't my favorite project provided an update recently?

Active projects: Check your favorite project’s forum. If there has not been a formal update in over six months or a short monthly update in a couple of months, then post a question in the forum.

Completed projects: Your favorite completed project probably doesn’t have any news to report at this time. Keep an eye on the forum for the project.

Will my computing time only help the FightAIDS@Home project?

Your device will contribute to whatever projects you choose; however, only certain projects will be available for mobile devices. You can select from the projects currently active at World Community Grid by visiting the My Projects page. There you can view all available projects, and choose those in which you want to participate.

Will my device only be working on the GO Fight Against Malaria project?

You get to decide which project or projects your computing time will help advance; however, only some projects are available for mobile devices. You can select from the active projects that are being performed on World Community Grid by visiting the My Projects page. Follow that link, and you can view all the available projects and choose those in which you want to participate.

What is the status of the Genome Comparison project?

The Genome Comparison project was completed in July, 2007. You may read about the Genome Comparison project here. Findings from the Genome Comparison research scientists will be posted here.

What is an intermittent project?

Intermittent projects are projects that will only periodically have work available to download. This could be because the project has finished but the researchers may not be finished analyzing all the results, and as such, may discover that they have to run a few more work units through the grid. This could also be because the project team may have periods where they cannot produce work as fast as the members are able to process their work.

Why is the Africa Rainfall Project opt-in only?

The Africa Rainfall Project requires significant computing power from each device: 1 GB of available memory and 1.5 GB of available disk space. Volunteers should make sure that their computers have these resources before opting in to the project.

Where are the Help Cure Muscular Dystrophy - Phase 2 FAQs?

FAQs about the project are in the Resesarch section under Project FAQs.

Where are the Help Cure Muscular Dystrophy FAQs?

FAQs about the project are in the Resesarch section under Project FAQs.

What is the status of the Human Proteome Folding project?

The first phase of the Human Proteome Folding Project was completed in July, 2006. You may read about the Human Proteome Folding Phase 1 results here.

What do the progress bars for each active project on the Research Page mean?

Every project on World Community Grid is at one of the following four stages:

• Just Launched - The project was launched on World Community Grid within the last few weeks.
• In Progress - The project is running regularly on World Community Grid and is not close to completion.
• Nearly Completed - The project is within a few weeks of finishing its work on World Community Grid.
• Completed - The project has completed its work on World Community Grid.

Which World Community Grid projects can be run on Android devices?

Please see this FAQ for World Community Grid projects currently running on Android devices.

Can you explain the screen savers?

You may find an explanation of the various project screen savers under the specific research project name found in the “Overview” section of our Help facility

What version of WRF was being used for the AfricanClimate@Home project?

AfricanClimate@Home presently uses WRF Model Version 2.2 (December 2006). In addition, this project is not using the Chemistry model of WRF.

How can I find the latest status on the FightAIDS@Home Project?

You may find the latest status on the FightAIDS@Home Project here.

Do World Community Grid projects involve animal testing?

So far, none of our past or current projects have involved animal testing while they were running on World Community Grid.

World Community Grid projects are considered basic research, which means that they are studying the foundations of a particular scientific subject rather than testing treatments in a lab. If a project is successful, it may lead to animal testing (typically by a separate research group) at some time in the future.

Why is my computer not getting as many work units for the Africa Rainfall Project as I want?

Due to the large file sizes of the input and output for this project, the number of tasks sent out per day will be much less than typical projects. For launch, we started out slow, and while the total number of tasks sent out per day may increase some as we get further in to the project, at this point we anticipate those increases to be minimal.

What is the difference between the Computing for Sustainable Water project and the Computing for Clean Water project?

The Computing for Sustainable Water project is studying how changes in human activities could help improve the quality of watersheds, critical for sustaining life and food sources. The Computing for Clean Water project is trying to develop less expensive water filters so that it would be more practical to produce clean drinking water from poor water sources.

I'm using the BOINC agent, how do I choose which project or projects my device processes work for?

You may select which projects you participate in using the My Projects page. This will set the projects you participate in for all of your devices. To set projects to run on certain device profiles, go to the Device Profiles page on our website. From there you can set each of your BOINC device profiles to run a different set of projects.

How do I limit the number of tasks assigned to one of my devices for a specific project?

Some projects can be very memory intensive, and some devices are not able to handle these memory intensive projects starting up multiple tasks for that project at a single time. Limiting the number of tasks allowed for a project will help to keep that from happening.

To limit the number of tasks for a specific project, please follow these steps:

1. Log in to your member account.
2. Click on Settings and then Device Manager.
3. Select the device profile you would like to make the changes to.
4. On the Device Profiles page, select Custom Profile.
5. Scroll down to the Project Limits section and set the tasks limits to your preferences.
6. Click the Save button.

What software does the Africa Rainfall Project use?

The Africa Rainfall Project uses the Weather Research & Forecasting (WRF) model for the research application. It is used to simulate weather conditions in a geographical region over a defined time period. The work for this project will be broken into small geographical regions of sub-Saharan Africa, and in the end each region will be simulated for one calendar year. 

WRF is a very large, mostly Fortran application, and the simulations being run require more resources than are typically used for a World Community Grid project. For this reason, volunteers will not be automatically opted into this project. 

Is there any way to estimate an end date for projects running on World Community Grid?

There are many variables with each project that determine how long it will last and how much work it will run on World Community Grid. These include:

• Change in research direction or project scope (e.g., results from work on World Community Grid that takes the project in a new direction)
• Increase or decrease in lab resources such as funding, staffing, etc
• New research findings from collaborators or other scientists in the same field 
• The pace at which computational work is being performed on World Community Grid

Researchers rarely know if or when these variables will come into play during their projects, which makes it challenging to estimate a project end date with any level of accuracy.

What is different about World Community Grid and other BOINC distributed computing projects?

Many of the BOINC projects are oriented toward one single research goal. And for those, the researchers have to set up their own infrastructure and manage the workload themselves. World Community Grid is able to accommodate multiple research projects. We run these projects for researchers from nonprofit organizations so that they do not have to manage the work and thus are able to focus on the science part of the research. For more information about how projects are selected to run on World Community Grid click here

To learn how to register and start participating in World Community Grid click here

Will World Community Grid ever run on a game box?

Running on game consoles requires specialized technical knowledge, plus the right kind of research project. The technical knowledge can be acquired but the research projects for game consoles must have a very small footprint.

Which World Community Grid research projects can run on GPUs?

For the latest on which World Community Grid research projects run on GPU, please refer to our system requirements.

What kinds of cancers are being studied in the Mapping Cancer Markers project?

Initially, we will focus on lung and ovarian cancer, followed by prostate, pancreatic and breast cancers. However, the project has been designed to accommodate other, less well-studied cancers if sufficient patient data exists.

What computers can run the "Discovering Dengue Drugs - Together" Project?

This project is distributed using the BOINC client, which is available for download on this site for computers with Windows, Macintosh, or Linux operating systems. For system requirements, click here.

What computers can run the "Discovering Dengue Drugs - Together" Project?

This project is distributed using the BOINC client, which is available for download on this site for computers with Windows, Macintosh, or Linux operating systems. For system requirements, click here.

How can I find the latest status on the Help Defeat Cancer Project?

The latest status on the Help Defeat Cancer Project may be found here.

What was the first phase of the Human Proteome Folding project all about?

Each project on World Community Grid contains its own information page. Click here for the Human Proteome Folding page.

Is there any way to express how close a project is to completion as a percentage? Can the progress bars show that a project is X% complete?

Over the years, we've found that most research teams don't load a certain number of work units into World Community Grid, let them run, and then declare the project complete. Rather, they create work units based on their initial research questions, then make adjustments to future work units based on their findings on World Community Grid and on outside research findings. This makes it impossible to accurately express project completion as a percentage.

Are the results produced by World Community Grid part of a commercial venture?

No. This is a philanthropic project, not for profit. The direct results of work done by the World Community Grid will be in the public domain.

When will the "Discovering Dengue Drugs - Together - Phase 2" project be completed?

Phase 1 began in August 2007 and finished in August 2009. Phase 2 started in February 2010 and may finish by the end of 2010.

How will my computer make a difference on this project?

While your computer is powered on, much of the time the processor inside your computer is just waiting for something to do, such as processing your next keystroke or mouse click. These idle times add up to a very large amount of processor time, when multiplied across millions of computers, that could be tapped and used for productive purposes such as this project. This can accelerate the research dramatically. Some of these projects would take hundreds or thousands of years to accomplish with the normal resources available to the scientists, and thus are likely not to even be attempted. World Community Grid and your contributions make projects such as these possible for the first time.

When will the DDD-T project be completed?

Phase 1 began in August, 2007 and finished in August, 2009. Phase 2 is expected to start in late 2009 and may finish by mid 2010.

What are the goals of the Microbiome Immunity Project?

The Microbiome Immunity Project aims to help scientists understand how trillions of bacteria in our bodies impact diseases such as Type 1 diabetes and Crohn's disease.

The primary goal of the project is therefore to generate a set of predicted protein structures of the entire human microbiome, containing around 3 million unique genes. This will help scientists determine the role played by these bacteria. Another goal is to share the results of the project with scientists around the world to further facilitate research on diseases implicated with the microbiome.

Why can I only get one task at a time for the Africa Rainfall Project?

We have set the default for the Africa Rainfall Project to one task at a time due to the larger than normal system requirements. If any volunteers wish to increase this value, please see the “How do I limit the number of tasks assigned ... for a specific project?” FAQ.

How does The Clean Energy Project benefit humanity?

The Clean Energy Project is focused on understanding the fundamental science of how flexible solar cells work, so scientists can design more efficient energy-related technologies. The results of the project will eventually help us reduce our dependence on fossil fuels to lower our carbon emissions, keep our air cleaner, and contribute to the fight against global warming. Our research will facilitate the development of cheap, flexible solar cell materials that we hope will be used worldwide.

What is the status of the Help Cure Muscular Dystrophy project?

The first phase of Help Cure Muscular Dystrophy was completed in June, 2007. The scientists are currently analyzing the phase 1 results in preparation for phase 2. We expect phase 2 to start in early 2009. You may read about the Help Cure Muscular Dystrophy project and the preparation for Phase 2 here.

Is the Mapping Cancer Markers project similar to the Help Conquer Cancer project?

Although both projects relate to cancer research, the Help Conquer Cancer project (run on World Community Grid from 2007-2013) focused on basic science - discovering principles of protein crystallization and helping to determine 3D structure of over 15,000 proteins. Knowing the protein structure helps scientists to understand their function and design drugs that may provide novel treatment options for multiple complex diseases, such as cancer.

The Mapping Cancer Markers project focuses on clinical application - discovering specific groups of markers that can be used to improve detection, diagnosis, prognosis and treatment of cancer. As a second goal, the comprehensive analysis of existing molecular profiles of cancer samples will lead to unraveling characteristics of such groups of markers - and in turn improving our understanding how to find them more efficiently.

Why is Phase 2 of the Clean Energy Project an opt-in project?

These calculations require work units that may run longer, have higher memory, disk space and data transfer requirements. Therefore, we are providing the users the option to opt-in to the project.

In addition, The Clean Energy Project is the first World Community Grid project to use an external server. That is, your result data is directly uploaded to the Harvard research server. Security checks are in place to make certain that uploaded data is transferred correctly and validated by the Harvard research server that is receiving the data. World Community Grid controls which servers the data is sent to and the Harvard servers will not send data files to the member machines.

Therefore, if you're interested in advancing the science of solar cells, please help us out in this great effort!

Why do I receive tasks / work units for research projects other than the projects I have selected on "My Projects" page?

On the server, there is a daemon called the 'feeder' which loads tasks into a shared memory segment every second. The shared memory segment can store up to 1000 tasks. When the scheduler receives a request from a client to fetch new tasks to work on, the scheduler only looks at this shared memory segment for tasks that it considers for sending. This is done because at any given time there are up to 1 million tasks available to send for a project. If the scheduler hit the database directly to search for tasks to send on each request, then the load on the database would be overwhelming.

The shared memory is divided into 'slots' that are allocated to the different projects that we have active. Only a task for that project can be assigned to a specific slot.

There are certain times each day when the slots for a given project in the shared memory segment become "full" of tasks that are designated for a particular platform (Linux or Windows). These usually only last a few minutes or seconds, but can sometimes last up to 30 minutes.

If for example, you are running Linux and the slots assigned to your selected research projects are full of tasks that are already assigned to Windows, then the server will treat it as no work is available for your selected research projects for you. (This is what triggers the 'tasks are assigned to another platform' message). If you have the 'send other' work preference checked on your preference settings, it will then look for other projects to send you tasks.

At this time, the best option for you is to uncheck the 'send other' preference if you do not want to receive work from other projects when the events described above occur.

How will the Computing for Sustainable Water project address the problem?

This project will, via a detailed simulation model of the entire Chesapeake Bay Watershed, test the impact of a large number of Best Management Practices (BMP)over a 20-year period. The proposed BMPs will be tested individually and in combination to assess their potential to effectively reduce the flow of nutrients and sediment into the Chesapeake Bay. Each of the various BMPs is expected to reduce the overall level of nutrients flowing into the Bay to some extent. However, scientists have no way of knowing in advance exactly how effective each might be. The project will provide an answer allowing policy-makers to choose those BMPs that will have the greatest impact.

What other technological applications will be relevant to this project?

Another technological application that will spawn from this project is the study of molecular electronics, where molecules are used for building electronic components. A good organic semiconductor for solar cells would also be good for potential applications in molecular electronics such as transistors. This means that The Clean Energy Project (CEP) has a potential to extend Moore's Law.

The CEP also plans to host a range of other calculations for cleaner energy capture and storage such as solar concentrator and polymer fuel cell. It is only with your help that researchers will be able to pursue these pure and applied directions of research.

What are the goals of the project and how are they being met?

The project’s primary goal is to identify drug candidates to control or cure certain types of childhood cancers. To meet this goal, the Smash Childhood Cancer research team is using World Community Grid to determine which of millions of chemical compounds may bind to certain target proteins or molecules involved with childhood cancers. These compounds would then be candidates for further testing and drug development, hopefully leading to treatments against these cancers.

To help achieve these goals, the research team plans to make the data from this project available to other scientists.

How are the goals of the project being met?

The Microbiome Immunity Project will meet its goals by using a computational research technique called protein structure prediction. This is a process through which computers simulate how a protein 1-dimensional sequence folds into its final 3-dimensional structure. (For more information about computational protein folding, see the Human Proteome Folding project.)

Knowing the structures of proteins of the microbiome can help researchers predict the functions of these proteins. An understanding of the role of these proteins will then help scientists develop drugs to control them or inhibit harmful interactions and therefore help treat diseases that originate in or are influenced by the human microbiome.

How are points used?

The calculation of Points is the method World Community Grid uses to measure your contribution to individual research projects running on World Community Grid. Points are one method for competitive comparison on the stats pages.

What is a Work Unit?

A work unit consists of data that represents a small part of an overall problem that the research project is trying to solve. Work Units are also referred to as Results.

What will happen with the data generated by all these calculations?

After the scientists have received all of the computed results for the project, they will analyze the data and publish their findings. The raw data and algorithms will be made publicly available at that time.

What will happen with the data generated by all these calculations?

After completion of the project and internal analysis by the research groups, all data will be made available on the Discovering Dengue Drugs-Together web site.

What will happen with the data generated by all these calculations?

After completion of the project and internal analysis by our groups, all data will be made available on the Discovering Dengue Drugs-Together web site.

What does The University of Nottingham logo in the screen saver represent?

The University of Nottingham, in the United Kingdom, was rated No. 8 for research power in the 2014 Research Excellence Framework and is the home of the research team behind the Help Stop TB project.