application repository

• name: Drug Discovery Grid
• domain: chemistry, drug discovery
• country: China
• author: Shanghai Institution of Material Medica and others
• institute:
• contacts:
• description: Drug Discovery Grid (DDG) exploits grid technology and grid computing resources to provide virtual drug screening services and drug chemistry information. One focus of drug discovery today is to search for pharmacologically active compounds from the vast compounds databases. Usually, only one or even none pharmaceutically active candidate can be found out of every 10000 compounds analysed. So, large chemical databases represent the most important factor for developing new drugs in a sustainable way. Big international pharmaceutical companies usually have chemical libraries of dozens of millions of compounds for automatic drug screening; on the other hand, chemical entities available are much less in China and this has seriously affected experimental drug discovery process. Computer-aided drug virtual screening can fill the gap and analyse candidate compounds for thousands of times. Because of the huge computation demand, grid technology (and namely CNGrid infrastructure and resources) was selected to implement a high throughput service for virtual drug screening.
• functionalities: DDG platform is was built on top of CNGrid, through the application and the extension of the CNGrid middleware, GOS, to design and establish productive operation-oriented DDG. Main funcnionalities include: new drug discovery grid platform system architecture oriented for productive operation; new drug discovery process based on grid workflow; task scheduling and transaction proceeding mechanisms oriented to novel drug discovery.
• middleware requirements: The deployment od DGG required the extension of GOS middleware in order to meet specific requirements:
  • Grid-based drug screening algorithm. New molecular docking methods, local protein flexibility predicting methods and new precise scoring functions, multi-scale molecular docking methods and optimization algorithms considering the flexibility of protein. Establishing reverse flexible protein molecular docking methods, non-redundant databases of protein structures and developing the corresponding software to be applied to find new drug targets. These modules will be assembled in the drug discovery grid platform.
  • interoperation of eterogeneous resources - in order to make different resources work together, consistency standard and specifications are needed, especially in terms of scheduling and management.
  • AAA infrastructure - As a public platform open to public professionals, a series of management technology should be set to achieve the level of productive operation. First, new drug discovery should provide means for user administration and authorization. At the  same time, a set of security mechanisms is needed. As the use of certain resources (including software and hardware) is not for free, grid accounting and billing is needed as well.

  • resources requirements:

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