------------------------------------------------------------------------------------ 
Virtual Laboratory: Molecular Modelling for Drug Design on Peer-to-Peer Grids
------------------------------------------------------------------------------------

          DesignDrug@Home -- A Data Intensive Science on P2P Grid! 

Peer-to-Peer Grids, enabling sharing of resources (computers, databases, instruments,
etc.) distributed across multiple organizations, have emerged as a promising platform
for executing large-scale resource intensive applications. The Virtual Laboratory
project at Monash University is exploring the use of Grid technologies for solving
compute and data intensive science applications in the area of molecular biology. The
project is carried out in collaboration with biologists and drug designers from the
Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia. 

Molecular modeling, basically, involves screening of millions of molecules of
chemical compounds in the Protein Data Bank (PDB) to identify those having potential
use in drug design. Screening each molecule in the target PDB is both compute and
data-intensive task. While performing docking, molecule information needs to be
extracted from the PDBs. The PDB databases are usually large in size--they need
storage space in the order of hundreds of megabytes to terabytes. Therefore, it is
infeasible to store them on all nodes in the Grid for processing.

The Virtual Laboratory project provides tools to selectively replicate PDBs on the
Grid and extract the required molecule information on demand with assistance from the
PDB Data-Grid broker that works in conjunction with Nimrod-G broker. The resource
brokering tools support deadline and computational economies based mechanisms for
deploying computations over the Grid. The Nimrod/enFusion declarative language and
GUI tools are being used to model molecular docking application for parameter
exploration.

An exploration of screening over two hundreds of molecules on target
electrocardiogram (ECE) endothelin converting enzyme involved in "heart stroke" has
been performed on World Wide Grid (WWG) test-bed resources spanning across
five continents (Australia, Asia, Europe, North America, and South America). The
results of this preliminary exploration have been exhibited at the recent IEEE/ACM
International Symposium on Cluster Computing and the Grid (CCGrid 2001) held in
Brisbane, Australia from May 15-18, 2001. The design of scalable tools for
data-brokering and large-scale experimentation on screening of millions of molecules
is currently underway. The project involves Monash University (Rajkumar Buyya, David
Abramson, Jon Giddy) and the Walter and Eliza Hall Institute of Medical Research (Kim
Branson). For further information on the Virtual Laboratory project, please browse: 
   http://www.csse.monash.edu.au/~rajkumar/dd@home/  
   http://www.csse.monash.edu.au/~rajkumar/ecogrid/
------------------------------------------------------------------------------------