Levitt D G, Banaszak L J
Department of Physiology, University of Minnesota, Minneapolis 55455.
J Mol Graph. 1992 Dec;10(4):229-34. doi: 10.1016/0263-7855(92)80074-n.
A new interactive graphics program is described that provides a quick and simple procedure for identifying, displaying, and manipulating the indentations, cavities, or holes in a known protein structure. These regions are defined as, e.g., the xo, yo, zo values at which a test sphere of radius r can be placed without touching the centers of any protein atoms, subject to the condition that there is some x < xo and some x > xo where the sphere does touch the protein atoms. The surfaces of these pockets are modeled using a modification of the marching cubes algorithm. This modification provides identification of each closed surface so that by "clicking" on any line of the surface, the entire surface can be selected. The surface can be displayed either as a line grid or as a solid surface. After the desired "pocket" has been selected, the amino acid residues and atoms that surround this pocket can be selected and displayed. The protein database that is input can have more than one protein "segment," allowing identification of the pockets at the interface between proteins. The use of the program is illustrated with several specific examples. The program is written in C and requires Silicon Graphics graphics routines.
本文描述了一种新的交互式图形程序，它提供了一种快速简单的程序，用于识别、显示和处理已知蛋白质结构中的凹陷、空洞或孔洞。这些区域被定义为，例如，半径为r的测试球体可以放置在不接触任何蛋白质原子中心的xo、yo、zo值，条件是存在一些x < xo和一些x > xo，此时球体会接触到蛋白质原子。这些口袋的表面使用 marching cubes算法的一种修改版本进行建模。这种修改能够识别每个封闭表面，这样通过“点击”表面的任何一条线，就可以选择整个表面。表面可以显示为线网格或实体表面。在选择了所需的“口袋”之后，可以选择并显示围绕该口袋的氨基酸残基和原子。输入的蛋白质数据库可以有多个蛋白质“片段”，从而能够识别蛋白质之间界面处的口袋。文中用几个具体例子说明了该程序的使用方法。该程序用C语言编写，需要Silicon Graphics图形例程。
