Computer Cluster for Computational and Structural Biology

用于计算和结构生物学的计算机集群

基本信息

批准号：
7217100
负责人：
Ronald Levy
金额：
$ 29.09万
依托单位：
RUTGERS, THE STATE UNIV OF N.J.
依托单位国家：
美国
项目类别：
财政年份：
2007
资助国家：
美国
起止时间：
2007-04-01 至 2009-03-31
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): This is a revised proposal to purchase a Computer Cluster to support nine NIH funded investigators carrying out research in computational and structural biology, structural genomics, and proteomics. We propose to acquire a 150 processor cluster based on the Linux operating system and the Opteron 280 AMD 64 bit dual-core processor. This is a much more cost efficient processor than the one available when the original proposal was submitted in March 2005; so that we are able to reduce the budget request by 40% without a significant decrease in the performance of the cluster we propose to acquire. Additionally, we provide more detailed information about the current computer facilities and the urgent need of these investigators to obtain NIH support to acquire the proposed instrument which will be used to update, centralize, and integrate the computational facilities which support the NIH funded projects described in this proposal. The projects for which the requested equipment will be used include: Effective Potentials and Sampling Methods for Protein Folding and Binding (R. Levy and E. Gallicchio), RNase H Inhibitors Targeting a Novel Site on HIV-1 RT (E. Arnold), NMR Investigation of Protein Folding and Misfolding (J. Baum), Automated NMR Protein Structure Determination and Refinement (G. Montelione), Multi-scale Modeling of Nucleic Acids (W. Olson), Structural Studies of RNA Polymerase Transcription Complexes and RNAP- Antibiotic Interactions (R. Ebright, E. Arnold, H. Berman), Parallel Single Molecule Data Analysis (D. Talaga), and Bioinformatic Modeling of Protein Interaction and Gene Regulation Networks (A. Sengupta). The projects described in this proposal all have computationally intensive components and due to their distributed and coarse-grained parallel nature, will greatly benefit from access to state-of-the-art hardware and a larger number of processors than is currently available to these investigators. The public health-related relevance of the projects described in this proposal 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.

描述（由申请人提供）：这是一项修订后的提案，旨在购买计算机集群，以支持 NIH 资助的 9 名研究人员开展计算和结构生物学、结构基因组学和蛋白质组学研究。我们建议购买一个基于Linux操作系统和Opteron 280 AMD 64位双核处理器的150个处理器集群。这是一种比 2005 年 3 月提交原始提案时可用的处理器更具成本效益的处理器；这样我们就能够将预算请求减少 40%，而不会显着降低我们建议购买的集群的性能。此外，我们还提供了有关当前计算机设施的更详细信息，以及这些研究人员迫切需要获得 NIH 支持来获取拟议仪器，该仪器将用于更新、集中和集成支持 NIH 资助项目的计算设施。这个建议。将使用所需设备的项目包括：蛋白质折叠和结合的有效潜力和采样方法（R. Levy 和 E. Gallicchio）、针对 HIV-1 RT 新位点的 RNase H 抑制剂（E. Arnold）、蛋白质折叠和错误折叠的 NMR 研究 (J. Baum)、自动 NMR 蛋白质结构测定和精化 (G. Montelione)、多尺度建模核酸 (W. Olson)、RNA 聚合酶转录复合物和 RNAP-抗生素相互作用的结构研究 (R. Ebright、E. Arnold、H. Berman)、并行单分子数据分析 (D. Talaga) 以及蛋白质的生物信息学建模相互作用和基因调控网络（A. Sengupta）。该提案中描述的项目都具有计算密集型组件，并且由于其分布式和粗粒度并行性质，将极大地受益于最先进的硬件和比这些研究人员目前可用的更多处理器。本提案中描述的项目与公共卫生相关的相关性在这些项目的两个主要目标中得到了强调。目标之一是进一步了解蛋白质的异常结构，这些结构是帕金森病、阿尔茨海默病和类似疾病的错误折叠疾病状态的特征。第二个主要目标是改进蛋白质结构和组装的表征方法，作为改进用于治疗艾滋病和其他疾病的基于结构的药物设计方法的基础。