Emekli Ugur, Schneidman-Duhovny Dina, Wolfson Haim J, Nussinov Ruth, Haliloglu Turkan
Polymer Research Center and Chemical Engineering Department, Bogaziçi University, 34342 Bebek, Istanbul, Turkey.
Proteins. 2008 Mar;70(4):1219-27. doi: 10.1002/prot.21613.
Proteins are highly flexible molecules. Prediction of molecular flexibility aids in the comprehension and prediction of protein function and in providing details of functional mechanisms. The ability to predict the locations, directions, and extent of molecular movements can assist in fitting atomic resolution structures to low-resolution EM density maps and in predicting the complex structures of interacting molecules (docking). There are several types of molecular movements. In this work, we focus on the prediction of hinge movements. Given a single protein structure, the method automatically divides it into the rigid parts and the hinge regions connecting them. The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins. The output can be used in applications such as flexible protein-protein and protein-ligand docking, flexible docking of protein structures into cryo-EM maps, and refinement of low-resolution EM structures. The web server of HingeProt provides convenient visualization of the results and is available with two mirror sites at http://www.prc.boun.edu.tr/appserv/prc/HingeProt3 and http://bioinfo3d.cs.tau.ac.il/HingeProt/.
蛋白质是高度灵活的分子。预测分子灵活性有助于理解和预测蛋白质功能，并提供功能机制的详细信息。预测分子运动的位置、方向和程度的能力可协助将原子分辨率结构与低分辨率电子显微镜密度图进行拟合，并预测相互作用分子的复杂结构（对接）。分子运动有几种类型。在这项工作中，我们专注于铰链运动的预测。给定单个蛋白质结构，该方法会自动将其划分为刚性部分以及连接它们的铰链区域。该方法采用弹性网络模型，该模型非常高效且已针对大量蛋白质数据集进行了验证。输出结果可用于诸如灵活的蛋白质 - 蛋白质和蛋白质 - 配体对接、将蛋白质结构灵活对接至冷冻电子显微镜图谱以及低分辨率电子显微镜结构的优化等应用中。HingeProt的网络服务器提供了结果的便捷可视化，可通过http://www.prc.boun.edu.tr/appserv/prc/HingeProt3和http://bioinfo3d.cs.tau.ac.il/HingeProt/这两个镜像站点访问。
