CONFORMATION AND DYNAMICS OF DEOXYRIBONUCLEIC ACIDS

希望了解结构和结构之间的关系 功能是结构生物学研究的核心。在 大分子水平，只有计算机模型才能处理 数量巨大的相互作用决定了结构和 动力学。该项目旨在阐明以下原则： 确定DNA序列如何影响DNA结构以及如何影响 结构受生物相关环境的影响 因素，如闭合成圈，超级卷曲，以及 与蛋白质和药物分子的相互作用。计算机模型是 是为研究这些问题而开发的。其中包括 一种预测和分析DNA的通用程序 在指定序列时设置。也在开发中 是一种新的程序，用于模拟分子中的DNA超级卷曲 大约5000个基准点长，结构分辨率为 基准面。它将被用来调查 序列、超螺旋压力和蛋白质结合在全球和 本地结构。正在开发新的算法，用于 静电效应的处理，用于简化处理 用于模拟构象转变，以及用于 在通用环境下进行分子动力学模拟 并行计算机。

The hope of understanding relationships between structure and function is at the heart of research in structural biology. At the macromolecular level, only computer models are capable of handling the enormous number of interactions that determine structure and dynamics. This project is aimed at elucidating the principles that determine how DNA sequence affects DNA structure and how that structure is affected by biologically relevant environmental factors, such as closure into circles, supercoiling, and interactions with proteins and drug molecules. Computer models are being developed for investigating these problems. Among these is a general purpose program for predicting and analyzing DNA structure when the sequence is specified. Also under development is a new program for modeling DNA supercoiling in molecules up to about 5000 basepairs long, with structural resolution to the basepair level. It will be used to investigate the effects of sequence, supercoiling pressure, and protein binding on global and local structure. New algorithms are being developed for the treatment of electrostatic effects, for the simplified treatment of solvation, for modeling conformational transitions, and for carrying out molecular dynamics simulations on general purpose parallel computers.