Ahmad Shandar, Sarai Akinori
Department of Biochemical Science and Engineering, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka-ken, Japan.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W104-7. doi: 10.1093/nar/gkh363.
We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions corresponding to the range of atomic coordinates. This box is then divided into cubic grids of selected size, which now have one or more charged atoms in them. This leaves each grid with a certain amount of charge. Cubic grids with more than a cutoff charge are then clustered using a hierarchical clustering method based on Euclidean distance. A tree diagram made from the resulting clusters indicates the distribution of charged and hydrophobic regions of the protein. Hydrophobic clusters are developed by grouping the positions of C(alpha) atoms of such residues. We propose that such a tree representation will be helpful in detecting protein-protein interfaces, structure similarity and motif detection.
我们开发了一种简单但功能强大的方法和网络服务器，用于快速定位蛋白质中的带电和疏水簇（http://www.netasa.org/qgrid/index.html）。对于带电簇，首先根据标准力场为蛋白质中的每个原子分配一个电荷。然后创建一个尺寸对应于原子坐标范围的盒子。接着将这个盒子划分为选定大小的立方网格，这些网格中现在有一个或多个带电原子。这使得每个网格带有一定量的电荷。然后使用基于欧几里得距离的层次聚类方法对电荷超过截止值的立方网格进行聚类。由所得簇生成的树形图表明了蛋白质带电和疏水区域的分布。疏水簇是通过对这些残基的C（α）原子位置进行分组来确定的。我们认为这种树形表示将有助于检测蛋白质 - 蛋白质界面、结构相似性和基序检测。
