Böhm H J
BASF AG, Ludwigshafen, Germany.
J Comput Aided Mol Des. 1994 Oct;8(5):623-32. doi: 10.1007/BF00123669.
It is shown that the computer program LUDI can be used to search large database of three-dimensional structures for putative ligands of proteins with known 3D structure. As an example, a subset of approximately 30,000 small molecules (with less than 40 atoms and 0-2 rotatable bonds) from the Fine Chemicals Directory has been used in the search for possible novel ligands for four different proteins (trypsin, streptavidin, purine nucleoside phosphorylase and HIV protease). For trypsin and streptavidin, known ligands or substructures of known ligands are retrieved as top-scoring hits. In addition, a number of new interesting structures are found in all considered cases. Therefore, the method holds promise to retrieve automatically protein ligands from a 3D database if the 3D structure of the target protein is known.
结果表明，计算机程序LUDI可用于在三维结构的大型数据库中搜索具有已知三维结构的蛋白质的假定配体。例如，已使用来自精细化学品目录的约30,000个小分子（原子数少于40个且可旋转键数为0 - 2个）的子集来搜索四种不同蛋白质（胰蛋白酶、链霉亲和素、嘌呤核苷磷酸化酶和HIV蛋白酶）的可能新型配体。对于胰蛋白酶和链霉亲和素，已知配体或已知配体的子结构作为得分最高的命中结果被检索到。此外，在所有考虑的案例中都发现了一些新的有趣结构。因此，如果目标蛋白质的三维结构已知，该方法有望从三维数据库中自动检索蛋白质配体。
