DYNAMIC STRUCTURE OF BIOMOLECULES IN SOLUTION

本子项目是利用由NIH/NCRR资助的中心赠款提供的资源的众多研究子项目之一。子项目和研究者（PI）可能已经从另一个NIH来源获得了主要资金，因此可以在其他CRISP条目中表示。列出的机构是中心的，不一定是研究者的机构。许多生物分子在溶液中具有柔韧性，这是通过核磁共振（NMR）来评估的。作为我们继续努力开发计算方法来阐明基于核磁共振数据的分子构象的一部分，我们提出了一种新的方法：多构象（“多拷贝”）改进，同时确定每个构象的种群。该方法的实现是基于miniCarlo和PDQPRO两个程序的结合。miniCarlo执行能量最小化和大都市蒙特卡罗模拟核酸。PDQPRO通过寻找计算和实验核磁共振参数之间的最佳拟合来确定预定义的潜在构象池的最佳概率分布。在RBVI中开发的Chimera软件包已广泛用于该项目生成的结构集成的图形表示和分析。

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. Many biological molecules are flexible in solution as assessed by nuclear magnetic resonance (NMR). As a part of our continuing effort to develop computational methods to elucidate molecular conformers based on NMR data, we have proposed a new approach: a multiple-conformer ("multiple-copy") refinement with simultaneous determination of each conformer's population. The implementation of this approach is based on combination of two programs, miniCarlo and PDQPRO. miniCarlo performs energy minimization and Metropolis Monte Carlo simulations for nucleic acids. PDQPRO determines the optimal probability distribution for a predefined pool of potential conformers by finding the best fit between calculated and experimental NMR parameters. The Chimera package developed within the RBVI has been used extensively for graphical representation and analysis of the structural ensembles generated by this project.