Social Docking Налаштування

[nikelong]

http://socialdocking.appspot.com/

Help Social Docking find potential drugs to treat Alzheimer's and AIDS. This project "is the first attempt ever to attempt virtual screening of Massive Compound Libraries entirely using JavaScript." The script "runs a Metropolis Monte Carlo Search with the ligand constrained to a binding site in the target. Enthalpy is calculated using the General Amber Force Field and Entropy is considered by taking the average of the Boltzmann distribution (how well the ligand 'tumbles down' the energy hypersurface)."
To participate in the project, open the project's URL in your HTML5-enabled web browser. The project runs a script in the background when you leave the web page open in your browser (you can view other web pages in other tabs) and exits the script when you exit the project web page. The script completes one work unit (a test of one ligand against three receptors) in about 10 minutes. Note: after a few minutes your web browser may display a message saying that a script is taking to long to complete and asking if you want to allow the script to run or to stop the script. Allow the script to run.

The project is the first to make use of HTML5 web workers (long-running scripts that run in the background and are not interrupted by user-interface scripts or user inputs). It also uses XmlHttpRequest level 2 (Cross-Origin Resource Sharing (CORS)) and WebGL math libraries.

[Death]

поскольку в браузере рагульно открывается скопирую сюда

SOCIAL DOCKING

Welcome to the Social Docking Project! This is a virtual screening application written entirely using HTML5.

Click Me to Start
-200020040060080010001200140016001800-500000.00000.0000500000.00001000000.00001500000.00002000000.00002500000.00003000000.0000« 1028908.7415kJ/mol

By leaving this browser window open, you are helping to find chemicals of pharmaceutical relevance towards Alzheimers, AIDS, and telomere maintenance. All computations are done by your web browser. Each ligand against 3 receptors takes about 10 minutes to run to completion. The goal is to finish 25,000 molecules by Jan 31, 2012.

To quit this program, just close this window.

To dual-wield, open this app in another window.

This app currently has issues with Facebook's Secure Browsing Feature. Please use socialdocking.appspot.com instead, or disable Secure Browsing

Tell the world about the Social Docking Project!
Oh no! It looks like your web browser is not compatible with Social Docking. Please use the latest version of Chrome, Firefox, Safari, or Opera for best results.

What is it?

The drug development pipeline is very expensive - it takes over 0.8 billion dollars for a pharmaceutical company to find, test, and introduce a drug into the market.

Virtual screening is a way to 'simulate' drug testing by using a supercomputer to narrow down drug candidates. Although this is far cheaper than the conventional pipeline, supercomputers don't grow on trees. There have been some efforts (Folding@home and SETI@home) to use volunteer computers, but these projects involve installing complicated software.

The Social Docking Project is the first attempt ever to attempt virtual screening of Massive Compound Libraries entirely using JavaScript.

Comparison with other VS solutions



local supercomputer

old-fashioned volunteer computing

social docking
First Introduced
1960
2000
2012
Accessible within 3 seconds?
User requirements
Operate master/slave distributed network
Install BOINC software, attach client to project, deal with Firewalls, troubleshoot
Press the 'Start' button
Cost
$25,000 - $300 million
$0
$0
how does it work?

Computing with web browsers poses several challenges. First, JavaScript (client-side web browser language) is not very fast. Furthermore, JavaScript shares the thread with the DOM, so user's web page freezes up if JavaScript runs too long.


That might have been in the case in 2008, but recent implementations of the HTML5 web workers in modern web browsers (Firefox, Chrome, Safari) allow background execution of code. Also, Google Chrome has a crazy fast V8 engine that compiles JavaScript to native machine code.


Behind the scenes: Web Workers run a Metropolis Monte Carlo Search with the ligand constrained to a binding site in the target. Enthalpy is calculated using the General Amber Force Field and Entropy is considered by taking the average of the Boltzmann distribution (how well the ligand 'tumbles down' the energy hypersurface).

more info

OS/Browser requirements?

None! As long as your computer/iPhone possesses the capability to push the start button, you should be all set. For best results, use Chrome/Firefox/Safari.

Some stats

Chemical (formula) currently being tested:CCC[C@@H](C1=NC2(CCCCC2)Cc3c1cccc3)C(=O)N

Algorithms used

Hückel's rule
Gasteiger Partial Charge Equalization
General Amber Force Field(Newtonian Mechanics using Quantum Mechanics force constants)
Metropolis Monte Carlo Search Algorithm
You should do _______ with your project!

I'm currently developing a lot of new features - many improvements coming in the future. All the code will be open-sourced with the GPL License a few months from now. However, I'm open to new ideas! Send me a FB message.

How much did this project cost?

One of the goals of this project was to spend this on the budget of a high school science fair project (which it is, after all). SocialDocking costs $0 to operate, but is limited in frontend instances by Google App Engine's pricing system.

Credits:

Special thanks to Nikolai and Chris from UCSF for fruitful discussion. Also a big thanks to iChemLabs for their cloud services.


Copyright 2011, Eric Jang

Copyright 2011, Eric Jang