DETECTION, DELINEATION, MEASUREMENT AND DISPLAY OF CAVITIES IN MACROMOLECULAR STRUCTURES
DETECTION, DELINEATION, MEASUREMENT AND DISPLAY OF CAVITIES IN MACROMOLECULAR STRUCTURES
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DOI：
10.1107/s0907444993011333
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发表时间：
1994-03-01
期刊：
影响因子：
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通讯作者：
JONES, TA
中科院分区：
文献类型：
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作者：
KLEYWEGT, GJ;JONES, TA
描述了一个计算机程序，VOIDOO，它可以用于研究腔，如它们发生在大分子结构（特别是蛋白质）。该程序可用于检测未知的空腔或描绘已知的空腔，其中任何一个都可能连接到正在研究的分子或分子组装体的外部。可选地，可以请求包含空腔形状描述的输出文件，该描述可以由晶体学建模程序0显示。此外，VOIDOO可用于计算分子的体积，并创建包含分子表面相关数据的文件，该文件也可使用0显示。对于P2髓磷脂蛋白、细胞视黄醇结合蛋白和纤维二糖水解酶II给出了VOIDOO的使用实例。最后，介绍了区分不同类型空洞的操作定义，并给出了评估准确性和提高空洞计算可比性的准则。
A computer program, VOIDOO, is described which can be employed in the study of cavities such as they occur in macromolecular structures (in particular, in proteins). The program can be used to detect unknown cavities or to delineate known cavities, either of which may be connected to the outside of the molecule or molecular assembly under study. Optionally, output files can be requested that contain a description of the shape of the cavity which can be displayed by the crystallographic modelling program 0. Additionally, VOIDOO can be used to calculate the volume of a molecule and to create a file containing data pertaining to the surface of the molecule which can also be displayed using 0. Examples of the use of VOIDOO are given for P2 myelin protein, cellular retinol-binding protein and cellobiohydrolase II. Finally, operational definitions to discern different types of cavity are introduced and guidelines for assessing the accuracy and improving the comparability of cavity calculations are given.