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* * * 8 蛋白质结构可视化工具与蛋白质结合分析 相关软件简介 * 常见结构可视化软件 100’s of visualization tools have been developed in bioinformatics. Many are specific to hardware such as microarray devices. Shareware utilities for PC’s PDB Viewer, WebMol, RasMol, Protein Explorer, Cn3D VMD, MolMol, MidasPlus, Pymol, Chime, Chimera * Application Feature Summary Feature RasMol Cn3D PyMol SWISS-PDBViewer Chimera Architecture Stand-Alone Plug-in Web-Enabled Web-enabled Web-enabled Manipulation Power Low High High High High Hardware Requirements Low/Moderate High High Moderate High Ease of Use High; command line Moderate Moderate High Moderate;GUI +command line Special Features Small Size; easy install Powerful GUI GUI; ray tracing Powerful GUI GUI; collaboration Output Quality Moderate Very high High High Very high Documentation Good Good Limited Good Very good Support Online; Users groups Online; Users groups Online; Users groups Online; Users groups Online; Users groups Speed High Moderate Moderate Moderate Moderate/Slow OpenGL Support Yes Yes Yes Yes Yes * Wireframe used to show individual chains: * Stick view showing atoms and bonds: * Surface View showing surface fields: * Ribbon view of secondary structure: * Distinct geometrical features by color: * For Protein interactions, we need a metaphor that reveals dynamics Haptic Joystick: Provides force feedback when user manipulates a molecule near another one. 3D Goggles combined with haptic gloves to feel electrostatic potentials and see tertiary structure dynamics. PyMol provides scripting that can produce a movie in 3D of the geometrical relationship between multiple proteins. Stereo view of interaction of two proteins. Scripting allows for the movement of individual molecules creating a movie. * * * 9 未来研究展望 为确定蛋白质组中的特定相互作用，我们还需要更多的软件工具。 我们需要新的复合工具管理复合体数据。 我们需要软件展示蛋白质间相互作用的动态关系。 * 途径 (调节网络) 预测 计算比较基因组学 文本 (文献) 挖掘 Small RNA 和反义调节 选择性剪切预测 计算代谢组学 BI紧迫研究领域 * 基因组语义学（Genome semantics） 膜蛋白结构预测 RNA 三级结构预测 翻译后修饰 动态调节网络 虚拟细胞/生物体模型 … (nobody knows)