OGFLEMM

Grid computing is one of the essential emerging technologies in the information technology community. Based on the experience with middleware tool implementations, like the GLOBUS toolkit and the UNICORE software, the Global Grid Forum (see www.gridforum.org) has standardised Open Grid Services Architecture (OGSA). As a result of the British e-science project (see http://www.rcuk.ac.uk/escience/ ), OGSA-DAI (Open Grid Services Architecture Data Access and Integration) extends OGSA by the remote access of data bases. The OGSA-DAI software is available as public domain software.

In OG-FLeMM NEC and SCAI will evaluate the usability of the OGSA-DAI implementation for distributed storage and analysis of molecular docking and molecular dynamics results. For this task a »molecular docking / molecular dynamics demonstrator« will be implemented, which emulates a part of the typical distributed data analysis work carried out by multinational pharmaceutical research organizations.

 

  • The following situation is the basis for the »molecular docking / molecular dynamics demonstrator«
  • In the course of the drug discovery and drug development process, identified candidate compounds (usually small molecules) undergo optimisation procedures and in silico design changes with the aim to improve binding to their pharmaceutical target proteins.
  • Amongst the in silico technologies used for this process, molecular docking tools and molecular dynamic simulation tools are widely used in the pharmaceutical industry. In the course of the FLEMM II project, a joint project of C&C Research Laboratories and Fraunhofer SCAI started in April 2003, a molecular docking tool (FlexX; a docking tool developed at SCAI) has been used to simulate the binding of several hundred compound structures to one target protein. The output from the FlexX runs have also been used as input for different molecular mechanics (MM) tools; the project aims at demonstrating an added value of the coupling of both procedures.
  • In OG-FLEMM, the project outlined here, we will design a database to store FlexX and MM tool results and to use the FLEMM scenario for testing database access in a distributed database setup. Communication between and retrieval from this database will be based on OGSA-DAI, the database management systems will be MySQL. Auxiliary database (e.g. for PDB conformation data) can be added to this setup.
  • The primary aim is to provide a repository for the refined docking and conformation results produced by iterated runs of the MM tools with different input parameters. The database will be designed so as to allow storage of the energy values along with the parameters that produced the respective energy record. Eventually the database is meant to allow ordering and retrieval of all results produced given a particular protein-compound combination in order to evaluate the plausibility or optimality of different modelling parameters.

 

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