Rueda Manuel, Orozco Modesto, Totrov Maxim, Abagyan Ruben
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
BMC Struct Biol. 2013 Dec 13;13:32. doi: 10.1186/1472-6807-13-32.
Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser.
BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin.
BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper.
蛋白质数据库（PDB）中的大多数蛋白质都是寡聚复合物，由两个或更多个通过旋转或螺旋对称结合的亚基组成。尽管文献中有大量的叠加工具，但我们找不到任何能够考虑旋转对称性并在网页浏览器中显示图形结果的工具。
BioSuper是一个免费的网络服务器，用于叠加并计算显示旋转对称性的蛋白质复合物的均方根偏差（RMSD）。据我们所知，BioSuper是同类工具中的第一个，它能在浏览器中即时交互式可视化图形结果，具备生物分子生成功能、不同层次的原子选择、基于序列和基于结构的叠加类型，并且是唯一考虑到显示对称性模糊的侧链中原子等效性的网络工具。BioSuper使用ICM程序功能作为叠加的核心，并将结果显示为文本、HTML表格和3D交互式分子对象，这些对象可通过免费插件在浏览器或安卓和iOS平台中可视化。
BioSuper是一个快速且实用的工具，可用于对显示旋转对称性的蛋白质和组件进行成对叠加。这个网络服务器是在我们自己尝试叠加柔性寡聚体时感到沮丧之后创建的。我们坚信，其用户友好且实用的设计对于需要叠加寡聚蛋白质（或任何蛋白质）的结构生物学家和计算生物学家来说将极具吸引力。所有用户均可在http://ablab.ucsd.edu/BioSuper免费使用BioSuper网络服务器。
