Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W440-4. doi: 10.1093/nar/gks535. Epub 2012 Jun 11.
We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.
我们开发了一个名为 PRince 的网络服务器，用于分析蛋白质 - RNA 界面的结构特征和物理化学性质。用户需要提交一个包含蛋白质和 RNA 分子复合物的原子坐标的 PDB 文件（以 '.pdb' 格式）。他们还应提及相互作用的蛋白质和 RNA 分子的链标识符。通过测量与溶剂接触的埋藏表面积来估计蛋白质 - RNA 界面的大小。对于给定的蛋白质 - RNA 复合物，PRince 计算相互作用表面的结构、物理化学和水合性质。服务器生成的所有这些参数都以表格形式呈现。相互作用的表面也可以使用 Jmol 等软件插件进行可视化。此外，还可以下载包含相互作用的蛋白质、RNA 和界面水分子的原子坐标列表的输出文件。PRince 生成的参数是新颖的，用户可以将它们与实验测定的生物物理和生化参数相关联，以更好地理解蛋白质 - RNA 识别过程的特异性。该服务器将不断升级，以包括更多的参数。PRince 是公开访问且免费使用的。可在 http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html 获得。
