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: 7601284
• 负责人: HAROLD A. SCHERAGA
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601284
• 关键词: CASP4 gene; CASP5 gene; CASP6 gene; CASP7 gene; Code; Computer Retrieval of Information on Scientific Projects Database; Development; Event; Exercise; Funding; Grant; Institution; Methods; Proteins; Protocols documentation; Research; Research Personnel; Resources; Running; Simulate; Source; Testing; Time; United States National Institutes of Health; base; caspase-3; concept; millisecond; molecular dynamics; protein structure prediction; research study

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. For the past several years, we have been developing a united residue force field UNRES. The UNRES force field has been derived as a potential of mean force of the united-residue chain and ultimately parameterized based on the concept of a hierarchical protein energy landscape. Protein structure prediction was demonstrated in extensive tests on known proteins and in four blind-prediction experiments CASP3, CASP4, CASP5, and CASP6 in years 1998, 2000, 2002, and 2004. Recently we implemented the UNRES force field in molecular dynamics. Initial results from UNRES molecular dynamics runs shows that we are able to simulate folding events which take place in a microsecond- or even a millisecond-time scale. Our research plan for the period APR/2006-MAR/2007 are: i) continuation of development of the molecular dynamics code for the UNRES force field; ii) continuation of the fine-tuning of the UNRES force field using a revised hierarchical potential-function optimization protocol; iii) enhancement of the capability of different global search methods for the UNRES force field; iv) participation in CASP7 exercise.

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 在过去的几年里，我们一直在开发一个联合的残余部队区域UNRES。UNRES力场被推导为联合残基链的平均作用力的势，并最终基于分层蛋白质能量景观的概念进行参数化。蛋白质结构预测在已知蛋白质的广泛测试中得到证实，并在1998、2000、2002和2004年的四个盲预测实验CASP3、CASP4、CASP5和CASP6中得到验证。最近，我们实现了分子动力学中的UNRES力场。UNRES分子动力学运行的初步结果表明，我们能够模拟在微秒甚至毫秒级发生的折叠事件。我们在APR/2006-MAR/2007期间的研究计划是：i)继续开发UNRES力场的分子动力学代码；ii)继续使用经修订的分层势函数优化协议对UNRES力场进行微调；iii)加强UNRES力场的不同全球搜索方法的能力；iv)参加CASP7活动。