Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ 08854, USA.
Nucleic Acids Res. 2010 Jan;38(Database issue):D267-74. doi: 10.1093/nar/gkp959. Epub 2009 Nov 11.
3DNALandscapes, located at: http://3DNAscapes.rutgers.edu, is a new database for exploring the conformational features of DNA. In contrast to most structural databases, which archive the Cartesian coordinates and/or derived parameters and images for individual structures, 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc. The data comprise all DNA-containing structures--both free and bound to proteins, drugs and other ligands--currently available in the Protein Data Bank. The web interface allows the user to link, report, plot and analyze this information from numerous perspectives and thereby gain insight into DNA conformation, deformability and interactions in different sequence and structural contexts. The data accumulated from known, well-resolved DNA structures can serve as useful benchmarks for the analysis and simulation of new structures. The collective data can also help to understand how DNA deforms in response to proteins and other molecules and undergoes conformational rearrangements.
3DNALandscapes 位于：http://3DNAscapes.rutgers.edu，是一个探索 DNA 构象特征的新数据库。与大多数仅归档单个结构的笛卡尔坐标和/或导出参数和图像的结构数据库不同，3DNALandscapes 支持跨多个结构进行构象信息搜索。该数据库包含广泛的结构参数和分子图像，这些参数和图像是使用 3DNA 软件包计算得出的，被证明对描述和理解 DNA 糖-磷酸主链、糖基侧基、碱基对、碱基对梯级、沟结构等的序列依赖性空间排列非常有用。这些数据包含了目前在蛋白质数据库中可用的所有含 DNA 的结构，包括与蛋白质、药物和其他配体结合的和未结合的 DNA。Web 界面允许用户从多个角度链接、报告、绘制和分析这些信息，从而深入了解不同序列和结构背景下的 DNA 构象、可变形性和相互作用。从已知的、分辨率良好的 DNA 结构中积累的数据可以作为分析和模拟新结构的有用基准。这些综合数据还有助于理解 DNA 如何响应蛋白质和其他分子而变形以及经历构象重排。
