Computer Cluster for Computational and Structural Biology

用于计算和结构生物学的计算机集群

• 批准号: 7794139
• 负责人: David A Case
• 金额: $ 43.32万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-22 至 2011-07-21
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7794139
• 关键词: AIDS/HIV problem; Acquired Immunodeficiency Syndrome; Alzheimer' s Disease; Binding; Cereals; Characteristics; Computer Simulation; Computers; Disease; Drug Design; Equipment; Funding; Goals; HIV; HIV vaccine; Investigation; Link; Methods; Nucleic Acids; Parkinson Disease; Proteomics; Public Health; Research; Research Personnel; Resources; Ribonuclease H; Sampling; Structure; Testing; Textiles; Transcriptional Regulation; base; computer cluster; computer studies; design; improved; inhibitor/antagonist; molecular dynamics; multi-scale modeling; protein folding; protein structure; public health relevance; structural biology; structural genomics

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.

描述（由申请人提供）：这是一份购买计算机集群的申请，以支持 NIH 资助的七个研究小组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 96 个计算节点，每个节点有两个四核处理器，总共 768 个处理器核心。计算节点通过低延迟 Infiniband 互连结构链接，以实现细粒度并行应用。将使用所需设备的项目包括： 生物分子动力学的关键测试（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）； HIV 疫苗和 HIV RNase H 抑制剂的计算机设计（E. Arnold 和 G.F. 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炼 (G. Montelione)；转录调控的计算研究（A. Morozov）；和核酸的多尺度建模（W. Olson）。这些项目都具有计算密集型组件，需要的计算机资源超出了罗格斯大学现有的资源。拟议扩展的一个关键方面是获得现代分子动力学和结构细化研究所需的更大并行能力。本申请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。 公共健康相关性：这是一份购买计算机集群的申请，以支持 NIH 资助的八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。与公共卫生相关的相关性包括研究表征帕金森病、阿尔茨海默病和类似疾病的错误折叠疾病状态特征的蛋白质异常结构，以及蛋白质结构和组装的表征，作为改进基于结构的药物设计方法的基础，以治疗帕金森病、阿尔茨海默病和类似疾病。艾滋病毒/艾滋病。

项目成果

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations.

• DOI: 10.1021/ct200684b
• 发表时间: 2012-01-10
• 期刊: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
• 影响因子: 5.5
• 作者: Lapelosa, Mauro;Gallicchio, Emilio;Levy, Ronald M.
• 通讯作者: Levy, Ronald M.

Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

结合能分布分析方法：用于结合模式预测和结合自由能估计的哈密顿复制品交换和扭转扁平化。

• DOI: 10.1021/acs.jctc.6b00134
• 发表时间: 2016
• 期刊: Journal of chemical theory and computation
• 影响因子: 5.5
• 作者: Mentes,Ahmet;Deng,Nan-Jie;Vijayan,RSK;Xia,Junchao;Gallicchio,Emilio;Levy,RonaldM
• 通讯作者: Levy,RonaldM