Hendlich M, Rippmann F, Barnickel G
Department of Pharmaceutical Chemistry, University of Marburg, Germany.
J Mol Graph Model. 1997 Dec;15(6):359-63, 389. doi: 10.1016/s1093-3263(98)00002-3.
LIGSITE is a new program for the automatic and time-efficient detection of pockets on the surface of proteins that may act as binding sites for small molecule ligands. Pockets are identified with a series of simple operations on a cubic grid. Using a set of receptor-ligand complexes we show that LIGSITE is able to identify the binding sites of small molecule ligands with high precision. The main advantage of LIGSITE is its speed. Typical search times are in the range of 5 to 20 s for medium-sized proteins. LIGSITE is therefore well suited for identification of pockets in large sets of proteins (e.g., protein families) for comparative studies. For graphical display LIGSITE produces VRML representations of the protein-ligand complex and the binding site for display with a VRML viewer such as WebSpace from SGI.
LIGSITE是一个全新的程序，用于自动且高效地检测蛋白质表面可能作为小分子配体结合位点的口袋状结构。通过在立方网格上进行一系列简单操作来识别口袋状结构。利用一组受体 - 配体复合物，我们证明LIGSITE能够高精度地识别小分子配体的结合位点。LIGSITE的主要优势在于其速度。对于中等大小的蛋白质，典型的搜索时间在5到20秒之间。因此，LIGSITE非常适合在大量蛋白质（如蛋白质家族）中识别口袋状结构以进行比较研究。为了进行图形显示，LIGSITE生成蛋白质 - 配体复合物以及结合位点的VRML表示，以便使用诸如SGI的WebSpace等VRML查看器进行显示。
