Grid-enabled Integration of Experimental Data and Simulations for Flexible Protein Docking

支持网格的实验数据和模拟集成,用于灵活的蛋白质对接

基本信息

  • 批准号:
    0450067
  • 负责人:
  • 金额:
    --
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
    Continuing Grant
  • 财政年份:
    2005
  • 资助国家:
    美国
  • 起止时间:
    2005-03-01 至 2009-02-28
  • 项目状态:
    已结题

项目摘要

The University of Notre Dame is awarded a grant to pursue grid-enabled integration of experimental data and simulations for flexible protein docking. The elucidation of interactions of a protein with ligands or other proteins is crucial for structure-based drug design and proteomics. Modeling the flexibility of proteins is substantially more accurate (and more expensive) than considering the protein as a rigid conformation. Current methodology effectively accommodates side chain motions. In this award this methodology is extended to accommodate larger motions using experimental data and multiscale simulations. The efficiency of docking will also be improved through integration of docking protocols with conformational sampling and analysis. These methods will be validated on HIV-1 protease, HIV-1 integrase, and Dihydrofolate Reductase (DHFR), for which abundant structural and dynamical data exists. Putative interactions will be validated through NMR experiments. This research will produce grid-based tools and a database for molecular simulations and docking accessible to the research community. A novel aspect of the database technology will be the efficient management of reliability and availability of storage on the grid. There will be interdisciplinary training and collaboration among students and the investigators.
圣母大学获得了一笔赠款,用于追求网格支持的实验数据和模拟的集成,以实现灵活的蛋白质对接。阐明蛋白质与配体或其他蛋白质的相互作用对于基于结构的药物设计和蛋白质组学至关重要。对蛋白质的柔性进行建模比将蛋白质视为刚性构象要准确得多(也更昂贵)。目前的方法有效地适应侧链运动。在这个奖项中,这种方法被扩展到使用实验数据和多尺度模拟来适应更大的运动。对接的效率也将通过整合对接协议与构象采样和分析来提高。这些方法将在HIV-1蛋白酶、HIV-1整合酶和二氢叶酸还原酶(DHFR)上进行验证,这些酶存在丰富的结构和动力学数据。将通过NMR实验验证假定的相互作用。这项研究将产生基于网格的工具和一个数据库,用于研究界可以访问的分子模拟和对接。数据库技术的一个新方面将是对网格上存储的可靠性和可用性进行有效管理。将有学生和调查人员之间的跨学科培训和合作。

项目成果

期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)

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Jesus Izaguirre其他文献

Atomic-Level Characterization of an Allosteric Gene Regulatory System
  • DOI:
    10.1016/j.bpj.2018.11.1183
  • 发表时间:
    2019-02-15
  • 期刊:
  • 影响因子:
  • 作者:
    Michael V. LeVine;Stefano Piana;Maxwell Tucker;Jesus Izaguirre;David E. Shaw
  • 通讯作者:
    David E. Shaw

Jesus Izaguirre的其他文献

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{{ truncateString('Jesus Izaguirre', 18)}}的其他基金

AF: Small: CCF: CISE: Advanced Grid-Enabled Algorithms for Discovering Protein Conformations
AF:小:CCF:CISE:用于发现蛋白质构象的先进网格算法
  • 批准号:
    1018570
  • 财政年份:
    2010
  • 资助金额:
    --
  • 项目类别:
    Standard Grant
CompBio: Simulation of self-emerging properties of coupled biochemical and cellular networks in social behavior of Myxobacteria
CompBio:模拟粘细菌社会行为中生化和细胞网络耦合的自生特性
  • 批准号:
    0622940
  • 财政年份:
    2006
  • 资助金额:
    --
  • 项目类别:
    Standard Grant
CAREER: Scalable Mathematical and Computational Models for Biomolecular Modeling
职业:生物分子建模的可扩展数学和计算模型
  • 批准号:
    0135195
  • 财政年份:
    2002
  • 资助金额:
    --
  • 项目类别:
    Continuing Grant

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