Computer Cluster for Computational Biology and Biophysics

计算生物学和生物物理学计算机集群

• 批准号: 8826397
• 负责人: Ronald Levy
• 金额: $ 44.23万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-19 至 2016-05-18
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8826397
• 关键词: AIDS/HIV problem; Algorithms; Anesthetics; Antibodies; Binding; Binding Proteins; Biochemistry; Biophysics; Computational Biology; Coupled; Data Set; Disease; Drug Design; Equilibrium; Equipment; Funding; Gated Ion Channel; Genomics; Grant; Human; Human Resources; Ion Channel; Linux; Markov chain Monte Carlo methodology; Membrane; Methods; Modeling; Nature; Performance; Population; Population Genetics; Postdoctoral Fellow; Process; Proteins; Public Health; Regulation; Research; Sampling; Staging; Statistical Methods; Structure; Students; TNFRSF5 gene; United States National Institutes of Health; Universities; base; computer cluster; design; improved; metalloenzyme; model design; molecular dynamics; programs; protein folding; protein structure; shared memory; simulation; structural biology; voltage

 DESCRIPTION: This is a proposal to purchase a Computer Cluster to support six NIH-funded research groups at Temple University (in total, more than 50 students, post-docs, and senior personnel) carrying out diverse projects spanning biophysics, biochemistry, structural biology, population genetics and genomics. Specifically, it is proposed to acquire a Linux cluster containing 40 compute nodes with four 16-core processors each, for 2560 processor cores in total. The cluster will provide the capacity that is optimized for the computing needs of the NIH supported projects described in this proposal. The projects for which the requested equipment will be used include: Protein-Ligand Binding and Allostery: Effective Potentials, Advanced Sampling Methods, and Applications (R.M. Levy); Permeation of Biologically Active Molecules and Regulation of Membrane Channels by Molecular Dynamics Simulations (M.L. Klein, V. Carnevale, and G. Fiorin); Optimization of New Statistical Scoring Terms in the Rosetta Program and Application to Antibody- Specific Computational Design (R. Dunbrack); Early Stages of Protein Folding Explored by Experimental and Computational Approaches (H. Roder and V. Voelz); Designing and Modeling Spiroligomer Based Metalloenzyme Mimics (C. Schafmeister), and Implementation of Statistical Methods for Human Population Genomics (E.J. Hey). These computationally intensive projects are currently supported by seven R01 grants, one P01 grant and one P50 grant. The requested hardware consists of a balanced combination of compute nodes with high- throughput low-latency InfiniBand interconnect and a high-performance storage appliance to accommodate projects which require shared memory in-node parallelization and loosely coupled message passing parallel or uncoupled independent processes operating on independent data sets. A key aspect of the proposed computer cluster acquisition is to obtain greater MPI parallel capabilities needed for modern atomic simulations of proteins using advanced sampling algorithms, molecular dynamics simulations of membranes and ion channels, and Markov Chain Monte-Carlo simulations employed in population genetics and genomics modeling. The public health-related relevance of the projects described in this proposal include improving methods for the characterization of protein structures (and assemblies) as a basis for structure based drug design for treatments of HIV/AIDS and other diseases, as well as understanding the nature of the binding of anesthetics to voltage-gated ion channels.



项目成果

Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses

• DOI: 10.1002/jcc.26078
• 发表时间: 2019-10
• 期刊: Journal of Computational Chemistry
• 影响因子: 3
• 作者: Y. Sakae;Bin W. Zhang;R. Levy;N. Deng

Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability.

用于预测突变对蛋白激酶稳定性影响的波茨哈密顿模型和分子动力学自由能模拟。

• DOI: 10.1021/acs.jpcb.3c08097
• 发表时间: 2024
• 期刊: The journal of physical chemistry. B
• 作者: Thakur,Abhishek;Gizzio,Joan;Levy,RonaldM
• 通讯作者: Levy,RonaldM

Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix

• DOI: 10.1021/acs.jctc.9b00740
• 发表时间: 2020-01-01
• 期刊: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
• 影响因子: 5.5
• 作者: Cui, Di;Zhang, Bin W.;Levy, Ronald M.
• 通讯作者: Levy, Ronald M.

Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure.

全局和局部机械特性控制 DNA 折纸纳米结构的核酸内切酶反应性。

• DOI: 10.1093/nar/gkaa080
• 发表时间: 2020
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Suma,Antonio;Stopar,Alex;Nicholson,AllenW;Castronovo,Matteo;Carnevale,Vincenzo
• 通讯作者: Carnevale,Vincenzo