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.

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。 在过去的几年中，我们一直在开发一个联合的残留力场。未恢复力场是作为统一链链的平均力的潜力，并最终基于层次蛋白能量景观的概念进行参数化。在对已知蛋白质的广泛测试中证明了蛋白质结构的预测，在1998年，2000年，2002年和2004年的四个盲目预测实验中，CASP4，CASP5和CASP6。 UNRES分子动力学运行的初始结果表明，我们能够模拟在微秒甚至毫秒尺度上发生的折叠事件。我们2006年4月/2007年4月期间的研究计划是：i）延续开发分子动力学代码针对未恢复力场； ii）使用修订的层次势函数优化方案来延续未恢复力场的微调； iii）增强了对未恢复力场的不同全局搜索方法的能力； iv）参加CASP7练习。