Computer Cluster for Computational and Structural Biology

描述(申请人提供)：这是一份购买计算机集群的申请，以支持七个由NIH资助的研究小组在计算和结构生物学、结构基因组学和蛋白质组学方面的研究。我们计划收购96个计算节点，每个节点有两个四核处理器，总共有768个处理器核。计算节点通过低延迟Infiniband互连交换矩阵进行链接，以实现细粒度并行应用。将使用所需设备的项目包括：生物分子动力学关键测试(D.Case)；蛋白质折叠和结合的有效电位和采样方法(R.Levy和E.Gallicchio)；艾滋病毒疫苗和艾滋病毒RNaseH抑制剂的电子设计(E.Arnold和G.F.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精细化(G.Montelione)；转录调控的计算研究(A.Morosov)；以及核酸的多尺度建模(W.Olson)。这些项目都有计算密集型组件，需要的计算机资源超过了罗格斯大学目前可用的资源。拟议的扩展的一个关键方面是获得现代分子动力学和结构优化研究所需的更大的并行能力。本申请书中描述的项目与公共卫生有关的相关性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氏症、阿尔茨海默氏症和类似疾病的错误折叠疾病状态。第二个主要目标是改进表征蛋白质结构和组装体的方法，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。 公共卫生相关性：这是一个购买计算机集群的申请，以支持NIH资助的八名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方面的研究。与公共卫生相关的研究包括对表征帕金森氏症、阿尔茨海默氏症和类似疾病的错误折叠疾病状态的蛋白质的异常结构的研究，以及对蛋白质结构和组装的表征，以此作为改进艾滋病毒/艾滋病治疗的基于结构的药物设计方法的基础。

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.