PDB-Explorer: a web-based interactive map of the protein data bank in shape space.
PDB-Explorer: a web-based interactive map of the protein data bank in shape space.
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DOI：
10.1186/s12859-015-0776-9
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发表时间：
2015-10-23
影响因子：
3
通讯作者：
Reymond JL
中科院分区：
文献类型：
--
作者：
Jin X;Awale M;Zasso M;Kostro D;Patiny L;Reymond JL
RCSB蛋白质数据库（PDB）提供了对实验确定的生物大分子（蛋白质，肽和核酸）的3D结构的公开访问。虽然有各种工具可用于探索PDB，但访问整个PDB的全球结构多样性和感知PDB结构之间的关系的选项仍然非常有限。设计了一个136维原子对蛋白质三维指纹图（3DP），用于在增加的通过空间距离上计数分类原子对，以表示PDB条目的分子形状。最近邻搜索的例子，举例说明能力的3DP相似性，以确定密切相关的生物分子，从小肽酶和大的多蛋白复合物，如病毒颗粒。采用主成分分析法在3DP空间中实现了PDB的可视化。3DP属性空间根据蛋白质和蛋白质组装体的3D形状相似性对它们进行分组，但仍显示出区分密切相关结构的精湛能力。一个名为PDB-Explorer的交互式网站，提供了一个3DP空间中的PDB彩色编码交互式地图。地图的每个像素都包含一个或多个PDB条目，当选择像素时，这些条目直接显示为带状图。PDB-Explorer网站允许对任何PDB条目或作为蛋白质类型PDB文件上传的任何结构进行3DP最近邻搜索。网站上的所有功能都以独立于平台的方式用JavaScript实现，并从服务器获取数据，每天更新最新的PDB内容，确保完整和最新的覆盖面。使用PDB-Explorer进行的基本上即时的3DP相似性搜索提供了与慢得多的3D比对算法相当的结果，并自动将来自相同超家族的蛋白质聚集在紧密的组中。PDB的化学空间分类的分子形状的基础上，获得使用新的原子对3D指纹蛋白质和基于Web的数据库的探索工具，包括交互式的颜色编码的PDB化学空间的地图和最近邻搜索工具中实现。PDB-Explorer网站可在www.cheminfo.org/pdbexplorer上免费访问，这是一个前所未有的机会，可以交互式地可视化和探索PDB的结构多样性。PDB在3DP空间中的地图，按重原子计数和形状进行颜色编码。 本文的在线版本（doi：10.1186/s12859-015-0776-9）包含补充材料，可供授权用户使用。
The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.cheminfo.org/pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB. ᅟMaps of PDB in 3DP-space color-coded by heavy atom count and shape. The online version of this article (doi:10.1186/s12859-015-0776-9) contains supplementary material, which is available to authorized users.