Computer Cluster for Computational and Structural Biology

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DESCRIPTION (provided by applicant): This is a application to purchase a Computer Cluster to support seven NIH-funded research groups carrying out research in computational and structural biology, structural genomics, and proteomics. We propose to acquire 96 compute nodes with two quad-core processors each, for 768 processor cores in total. Compute nodes are linked by a low-latency Infiniband interconnect fabric for fine-grained parallel applications. The projects for which the requested equipment will be used include: Critical Tests of Biomolecular Dynamics (D. Case); Effective Potentials and Sampling Methods for Protein Folding and Binding (R. Levy and E. Gallicchio); In silico design of HIV vaccines and HIV RNase H inhibitors (E. Arnold and G.F. Arnold); NMR Investigation of Protein Folding and Misfolding (J. Baum); Automated NMR Protein Structure Determination and Refinement (G. Montelione); Computational studies of transcription regulation (A. Morozov); and Multi-scale Modeling of Nucleic Acids (W. Olson). These projects all have computationally intensive components that require computer resources beyond those available now at Rutgers. A key aspect of the proposed expansion is to obtain greater parallel capabilities needed for modern molecular dynamics and structure refinement studies. The public health-related relevance of the projects described in this application is highlighted in the two major goals of these projects. One goal is to further the understanding of aberrant structures of proteins that characterize misfolding disease states characteristic of Parkinson's, Alzheimer's, and similar diseases. A second major goal is to improve methods for the characterization of protein structures and assemblies as a basis for improving methods of structure based drug design for treatments of AIDS and other diseases. PUBLIC HEALTH RELEVANCE: This is a application to purchase a computer cluster to support eight NIH-funded investigators carrying out research in computational and structural biology, structural genomics, and proteomics. The public health related relevance includes study of aberrant structures of proteins that characterize misfolding disease states characteristic of Parkinson's, Alzheimer's, and similar diseases, and the characterization of protein structures and assemblies as a basis for improving methods of structure-based drug design for treatment of HIV/AIDS.