Department of Computer Sciences, University of Wisconsin-Madison Madison, WI 53715, USA.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W595-601. doi: 10.1093/nar/gkq398. Epub 2010 May 12.
The region surrounding a protein, known as the surface of interaction or molecular surface, can provide valuable insight into its function. Unfortunately, due to the complexity of both their geometry and their surface fields, study of these surfaces can be slow and difficult and important features may be hard to identify. Here, we describe our GRaphical Abstracted Protein Explorer, or GRAPE, a web server that allows users to explore abstracted representations of proteins. These abstracted surfaces effectively reduce the level of detail of the surface of a macromolecule, using a specialized algorithm that removes small bumps and pockets, while preserving large-scale structural features. Scalar fields, such as electrostatic potential and hydropathy, are smoothed to further reduce visual complexity. This entirely new way of looking at proteins complements more traditional views of the molecular surface. GRAPE includes a thin 3D viewer that allows users to quickly flip back and forth between both views. Abstracted views provide a fast way to assess both a molecule's shape and its different surface field distributions. GRAPE is freely available at http://grape.uwbacter.org.
蛋白质周围的区域，称为相互作用表面或分子表面，可以为其功能提供有价值的见解。不幸的是，由于它们的几何形状和表面场的复杂性，这些表面的研究可能会很慢且困难，并且重要的特征可能难以识别。在这里，我们描述了我们的 GRaphical Abstracted Protein Explorer，或 GRAPE，这是一个允许用户探索蛋白质抽象表示的网络服务器。这些抽象表面有效地降低了大分子表面的细节水平，使用专门的算法去除小的凸起和凹陷，同时保留大规模的结构特征。标量场，如静电势和疏水性，被平滑化以进一步降低视觉复杂性。这种全新的观察蛋白质的方法补充了更传统的分子表面视图。GRAPE 包括一个薄的 3D 查看器，允许用户在这两种视图之间快速来回翻转。抽象视图提供了一种快速评估分子形状及其不同表面场分布的方法。GRAPE 可在 http://grape.uwbacter.org 免费获得。
