Modern biology requires new approaches to biomolecular simulation. With nearly 200 000 protein sequences in the genomic databases, and over 33 000 structures deposited in the Protein Data Bank, single simulations of a single protein do not address the needs of contemporary biology. We are developing tools that will enable biomolecular simulations to provide an essential link between structural genomics and systems biology. In particular, the simulation community has to addressing three key areas of simulation technology: high-throughput simulations for high-performance computing, a grid-enabled database for comparative analysis of simulation data, and multi-scale biomolecular simulations ranging from the quantum-mechanical to the meso-scale. That is, we need to be ready to provide both the computational infrastructure and pharmaceutically relevant test cases to demonstrate the validity of this new approach. BioSimGrid, as a distributed database for biomolecular simulations, provides the keystone in the endeavour.
Visualisation and data handling methods: Database
Simulation software: Gromacs
Visualisation and data handling software: Xmgrace
Software Engineering Tools: CVS
Programming languages and libraries: Python
Computational platforms: Linux
Transdisciplinary tags: e-Research