Drug Discovery
- Different ligands (small molecules) docked in the binding pocket of a protein involved in the metabolism of a maleria virus.
The scenario is a distributed docking workflow involving docking tools from Chinese participants as well as docking tools from European participants aiming at an improved result by combining results of several docking tools for the same targets.
Based on the interconnected infrastructure and middleware, BRIDGE has extended the workflow-based B2B collaboration infrastructure developed within the 
SIMDAT Pharma activity along two dimensions. This first has enabled the execution of compute intensive applications for high throughput virtual screening. The second has enabled interoperability across heterogeneous Grid middlewares in Europe and China. In doing so, the project has made a number of key contributions. The first contribution was developing a suite of novel grid-based application integration tools that focus on algorithmic interoperability between different protein docking tools. The second contribution was the successful demonstration of using the middleware and tools in conducting novel scientific experiments for Bird Flu and Malaria. The third contribution was deploying the BRIDGE infrastructure in other parts of the world, namely Egypt. which is currently one of the countries most affected by the Bird Flu epidemic.
Deployment of the Pharma prototype
Virtual Screening and Protein Docking
Protein docking aims at positioning of small molecules (potential drugs) into the binding site of a target protein (associated with a specific disease). For this, one has to screen a large number of chemical compounds/ligands against target receptors.
The existing protein docking tools (such as FlexX, DOCK, AutoDock, GasDock, ..) operate based on different principals, and the docking results vary based on the specific tool or algorithm used.
DockFlow aims at constructing an interoperable grid-based virtual screening platform for drug discovery based on integration of four protein docking tools (FlexX, Autodock, DOCK and GAsDOCK) executing on a mix of European and Chinese Grid middleware.