THERMODYNAMICS OF PROTEIN-DNA & LIGAND-DNA COMPLEXES

这个项目的目标是开发和应用计算方法来重现， 理解和预测分子识别的结构和化学方面 在EcoRV酶-DNA和小配体-DNA复合物中。我们将使用这种方法与蛋白质（EcoRV）与DNA和小配体：放线菌素，吖啶，netropsin，呋喃咪唑啉相互作用。我们将使用这些系统的实验数据作为评估理论的关键准则。理解这里提出的系统中的识别，特别是在EcoRV-DNA复合物中的识别，将进一步实现NIH资助的长期目标，即使计算机方法可靠并具有真正的预测性，以便将其用作理解分子相互作用以及药物设计过程的重要工具。

The goal of this project is to develop and apply computational methods to reproduce, understand and predict structural and thermodynamical aspects of molecular recognition in the EcoRV enzyme-DNA and the small ligand-DNA complexes. We will use this methodology with a protein (EcoRV) interacting with DNA and small ligands: actinomycin, acridine, netropsin, furimidazoline. We will use the available experimental data on these systems as a critical guideline to evaluate the theory. Understanding recognition in the systems proposed here, especially in the EcoRV-DNA complex, will further the long term goal of the parent NIH grant, which is to make the computer approaches reliable and truly predictive in order to use them as an important tool in understanding molecular interactions as well as in the drug design process.