DEVELOPMENT AND APPLICATION OF A HIERARCHICAL PROTOCOL FOR AB INITIO PREDICTION

从头预测的分层协议的开发和应用

• 批准号: 7723114
• 负责人: HAROLD A. SCHERAGA
• 金额: $ 0.05万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723114
• 关键词: Amino Acid Sequence; Biochemical Process; Bioinformatics; Cereals; Computational Biology; Computer Retrieval of Information on Scientific Projects Database; Development; Funding; Grant; Institution; Lead; Methodology; Pathway interactions; Physics; Property; Proteins; Protocols documentation; Research; Research Personnel; Resources; Source; Structure; Thermodynamics; United States National Institutes of Health; base; molecular dynamics; protein structure; three dimensional structure

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Most of current research in computational biology and bioinformatics is focused on predicting the three-dimensional structure of proteins. Using different approaches, researchers are trying to develope methodology for predicting protein structure based only on amino acid sequence. However, three-dimensional structure alone is not sufficient to understand many biochemical processes which involve proteins. Research presented in this proposal is based on parametrization of our physics-based coarse-grained force-field UNRES, using information not only about the three-dimensional structure of the native state of proteins but also about their folding mechanism and thermodynamic stability. We expect that such parametrization and extensive conformational space search using molecular dynamics will enable us to simultaneously predict two protein properties: structure and thermodynamic stability of the native state and folding pathway(s) which lead from the unfolded to the folded state.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。子弹和 调查员（PI）可能已经从其他NIH来源获得了主要资金， 因此可以在其他清晰的条目中代表。列出的机构是 对于中心，这不一定是调查员的机构。 当前在计算生物学和生物信息学方面的大多数研究都集中在预测蛋白质的三维结构上。使用不同的方法，研究人员正在尝试开发仅基于氨基酸序列预测蛋白质结构的方法。但是，仅三维结构就不足以理解许多涉及蛋白质的生化过程。该提案中提出的研究基于我们基于物理学的粗粒力场unres的参数化，不仅使用有关蛋白质天然状态的三维结构的信息，而且还涉及其折叠机制和热力学稳定性。我们预计，使用分子动力学的这种参数化和广泛的构象空间搜索将使我们能够同时预测两种蛋白质特性：天然状态的结构和热力学稳定性和折叠途径（S）（s），从展开到折叠状态。