Computer Cluster for Computational and Structural Biology

描述（由申请人提供）：这是一份购买计算机集群的修订提案，以支持9名NIH资助的研究人员进行计算和结构生物学，结构基因组学和蛋白质组学的研究。我们建议购买一个基于Linux操作系统的150处理器集群和Opteron 280 AMD 64位双核处理器。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；因此，我们能够在不显著降低我们提议收购的集群性能的情况下，将预算请求减少40%。此外，我们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支持以获得提议的仪器，该仪器将用于更新，集中和整合支持本提案中描述的NIH资助项目的计算设施。所要求的设备将用于的项目包括：蛋白质折叠和结合的有效电位和采样方法（R. Levy和E. Gallicchio），靶向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核磁共振研究（J. Baum），自动核磁共振蛋白质结构测定和改进（G. Montelione），核酸的多尺度建模（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）和蛋白质相互作用和基因调控网络的生物信息学建模（A. Sengupta）。本提案中描述的项目都具有计算密集型组件，并且由于它们的分布式和粗粒度并行性质，将大大受益于访问最先进的硬件和比这些研究人员目前可用的更多数量的处理器。本提案中所述的项目与公众健康相关，在这些项目的两个主要目标中得到强调。一个目标是进一步了解蛋白质的异常结构，这些结构表征了帕金森病、阿尔茨海默病和类似疾病的错误折叠疾病状态。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。

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.