Ligand based virtual screening using Screen3D
Fully flexible 3D alignment method without the need for sampling the conformational space is presented. This approach offers advantages over methods that rely on multiple conformations. (1) Higher accuracy is achieved, since unlike discrete sampling it is not prone to missing optimal conformation. (2) Smaller database size is needed, pre-calculated conformers are not stored. The alignment procedure maximizes the intersection of the volume of the molecules being aligned. These volumes can be colored by atomic properties enabling the use of various similarity scores, like shape-, chemical- and biological similarity. Similarity scores serve as the basis for 3D virtual screening. The calculation of 3D similarities is computationally intensive. In order to achieve high performance fast pre-filtering by 3-dimensional molecular descriptors has been introduced. These shape descriptors are pre-calculated by the alignment machinery itself in an initialization stage.