Comparative Molecular Trajectory Analysis
EMSL Project ID
13307
Abstract
The large-scale simulation of biological systems as an integral component of a systems approach to biological research can only be accomplished if the emphasis in this field shifts to greater depth through the development and use of more accurate physical models, greater complexity by including more realistic, multi-component environments, and greater breadth through the use of comparative analysis methods that allow the simultaneous analysis of multiple molecular trajectories. In particular the efficient comparative analysis of multiple trajectories is a data intensive computing application that will be enabled through the use of large memory architectures. Our approach will be to develop and analyze new algorithms that will allow biomolecular simulation studies to be responsive to the challenges of post-genomic biological research. Just like in the case of the analysis of the large data sources created by the new high-throughput technologies, biomolecular simulations contribute to the progress in biology through comparative analysis. The continuing increase in available protein structures allows the comparative analysis of the role of structure and conformational flexibility in protein function, and is the foundation of the discipline of structural bioinformatics. This creates the opportunity to derive general findings from the comparative analysis of molecular dynamics simulations of a wide range of proteins, protein-protein complexes and other complex biological systems. Because of the importance of protein conformational dynamics for protein function, it is essential that the analysis of molecular trajectories is carried out using a novel, more integrative and systematic approach. For example, only with an integrated approach such as proposed here will it be possible to determine the role of common protein folds in otherwise unrelated proteins, or the effect of a common environment such as a membrane matrix on the transport and signaling properties of membrane proteins.
Project Details
Project type
Capability Research
Start Date
2005-02-02
End Date
2006-12-06
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members