AANT: the Amino Acid-Nucleotide Interaction Database
AANT: the Amino Acid-Nucleotide Interaction Database
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DOI：
10.1093/nar/gkh128
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Ellington, AD
中科院分区：
文献类型：
--
作者：
Hoffman, MM;Khrapov, MA;Ellington, AD
我们已经创建了一个氨基酸-核苷酸相互作用数据库（AANT; http://aant.icmb.utexas）。Edu/)，从实验确定的蛋白质-核酸结构中对所有氨基酸-核苷酸相互作用进行分类，并为用户提供图形界面，以便将这些相互作用可视化。AANT通过从蛋白质数据库的结构中提取单个氨基酸-核苷酸相互作用，将这些相互作用组合并叠加到多个结构文件中（例如20个氨基酸X 5个核苷酸），并将结构相似的相互作用分组为更容易识别的簇，从而实现这一目标。使用Chime网页浏览器插件，用户可以查看叠加和集群的3D表示。氨基酸-核苷酸相互作用数据的独特收集和表示有助于在更基本的水平上理解蛋白质-核酸相互作用的特异性，并允许比较其他极端不同的结构集。此外，通过模块化表示控制结合特异性的基本相互作用，可能证明更好地设计核酸结合蛋白是可能的。
We have created an Amino Acid-Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate. AANT accomplishes this by extracting individual amino acid-nucleotide interactions from structures in the Protein Data Bank, combining and superimposing these interactions into multiple structure files (e.g. 20 amino acids X 5 nucleotides) and grouping structurally similar interactions into more readily identifiable clusters. Using the Chime web browser plug-in, users can view 3D representations of the superimpositions and clusters. The unique collection and representation of data on amino acid-nucleotide interactions facilitates understanding the specificity of protein-nucleic acid interactions at a more fundamental level, and allows comparison of otherwise extremely disparate sets of structures. Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins.