Prioritized Assembly in Protein Conformational Search

蛋白质构象搜索中的优先组装

基本信息

  • 批准号:
    6482093
  • 负责人:
  • 金额:
    $ 9.89万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2002
  • 资助国家:
    美国
  • 起止时间:
    2002-05-28 至 2003-05-27
  • 项目状态:
    已结题

项目摘要

An efficient and effective conformational search method is essential for solving the computational protein folding problem. Prevalent conformational search models are fast but incomplete. Proposed here is an exhaustive enumeration-based search method that combines a focus on the most promising search paths with a complete coverage of the conformational space. The search is a prioritized building-up process: Structural templates of low energy are generated for short segments of the chain. Structural elements, either templates or individual residues, are added to a growing conformation one at a time. The addition of a structural element is prioritized on its energetical contribution one at a time. The addition of structural element is prioritized on its energetical contribution to the conformation as a whole. Simple templates such as tight turns, helices or strands form packing clusters such as hairpins and beta-sheets. A finished conformation is often the assembly of packing clusters. Such efficiency is achieved by pruning provably unpromising search branches at each building-up step. Phase I will implement the architecture of prioritized assembly-based search, demonstrating the feasibility of the approach. Phase II will develop algorithms for computing tight lower bounds of conformational energy, which are crucial for effective branch-and-bound search. Phase III will develop a comprehensive conformational search program for computational protein folding: PROPOSED COMMERCIAL APPLICATION: The primary market will be the academic research labs and technology concerns that need diverse sets of possible conformations for investigating peptides, proteins and protein-protein complexes. An additional market is the research labs that need near native or misfolded protein structures (decoys) for testing and improving their energy potentials and search methods.
高效的构象搜索方法是解决蛋白质折叠问题的关键。流行的构象搜索模型是快速但不完整的。这里提出的是一个详尽的枚举为基础的搜索方法,结合了最有前途的搜索路径的构象空间的完整覆盖的重点。搜索是一个优先级的建立过程:为链的短段生成低能量的结构模板。结构元素,无论是模板或单个残基,被添加到一个不断增长的构象一次一个。一个结构元素的添加是根据其能量贡献一次一个地优先考虑的。结构元素的添加优先考虑其对整体构象的能量贡献。简单的模板,如紧转弯,螺旋或股形成包装集群,如发夹和β-片。一个完成的构象往往是组装集群。这样的效率是通过在每个构建步骤中修剪可证明为没有希望的搜索分支来实现的。第一阶段将实现基于优先级的汇编搜索的架构,证明该方法的可行性。第二阶段将开发计算构象能严格下限的算法,这对于有效的分支定界搜索至关重要。第三阶段将为计算蛋白质折叠开发一个全面的构象搜索程序:拟议的商业应用:主要市场将是学术研究实验室和技术关注,需要不同的可能构象集,用于研究肽,蛋白质和蛋白质-蛋白质复合物。另一个市场是需要接近天然或错误折叠蛋白质结构(诱饵)的研究实验室,以测试和改进其能量潜力和搜索方法。

项目成果

期刊论文数量(1)
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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KAIZHI YUE其他文献

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{{ truncateString('KAIZHI YUE', 18)}}的其他基金

Prioritized Assembly in Protein Conformational Search
蛋白质构象搜索中的优先组装
  • 批准号:
    7216276
  • 财政年份:
    2002
  • 资助金额:
    $ 9.89万
  • 项目类别:
Prioritized Assembly in Protein Conformational Search
蛋白质构象搜索中的优先组装
  • 批准号:
    7056379
  • 财政年份:
    2002
  • 资助金额:
    $ 9.89万
  • 项目类别:
Prioritized Assembly in Protein Conformational Search
蛋白质构象搜索中的优先组装
  • 批准号:
    7394915
  • 财政年份:
    2002
  • 资助金额:
    $ 9.89万
  • 项目类别:
CONSTRAINTS ON PROTEIN SECONDARY STRUCTURE PACKING
蛋白质二级结构包装的限制
  • 批准号:
    6456831
  • 财政年份:
    2001
  • 资助金额:
    $ 9.89万
  • 项目类别:
CONSTRAINTS ON PROTEIN SECONDARY STRUCTURE PACKING
蛋白质二级结构包装的限制
  • 批准号:
    6347993
  • 财政年份:
    2000
  • 资助金额:
    $ 9.89万
  • 项目类别:
MODELING SECONDARY STRUCTURE ASSEMBLY IN PROTEIN CONFORMATIONAL SEARCH
蛋白质构象搜索中二级结构组装建模
  • 批准号:
    6119291
  • 财政年份:
    1999
  • 资助金额:
    $ 9.89万
  • 项目类别:
CONSTRAINTS ON PROTEIN SECONDARY STRUCTURE PACKING
蛋白质二级结构包装的限制
  • 批准号:
    6220363
  • 财政年份:
    1999
  • 资助金额:
    $ 9.89万
  • 项目类别:
MODELING SECONDARY STRUCTURE ASSEMBLY IN PROTEIN CONFORMATIONAL SEARCH
蛋白质构象搜索中二级结构组装建模
  • 批准号:
    6280312
  • 财政年份:
    1998
  • 资助金额:
    $ 9.89万
  • 项目类别:
COMPUTATIONAL METHODS FOR GLOBAL MINIMUM ENERGY CONFORMATIONS IN PROTEINS
蛋白质全局最小能量构象的计算方法
  • 批准号:
    6250515
  • 财政年份:
    1997
  • 资助金额:
    $ 9.89万
  • 项目类别:
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