MOLECULAR DYNAMICS SIMULATIONS OF NUCLEIC ACIDS: STRUCTURE, MOTIONS, SOLVATION

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。 我们提出的研究包括基于计算机模拟和相关理论方法的基于分子模拟的DNA和RNA核酸及其与蛋白质的络合物的动力学结构的研究。在DNA和RNA系统上进行分子建模和模拟的总体可靠性取决于计算结果的明显准确性。因此，本研究的重点之一是对最详细的计算建模形式之一--全原子分子动力学(MD)模拟的关键验证和评估。拟议项目期的另一个重点将是与MD进行自由能计算，以便更直接地探讨关于核酸结构及其复合体的稳定性和构象平衡的各种问题。

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. Our proposed research involves studies of the dynamical structures of DNA and RNA nucleic acids and their complexes with proteins based on molecular modeling via computer simulation and related theoretical approaches. The overall reliability of molecular modeling and simulation on DNA and RNA systems depends critically on the demonstrable accuracy of the calculated results. Thus, one of the focal points of this research is critical validation and assessment of one of most detailed form of computational modeling, all-atom molecular dynamics (MD) simulation. An additional emphasis in the proposed project period will be the articulation of free energy calculations with MD in order to approach more directly diverse questions about stability and conformational equilibria of nucleic acids structures and their complexes.