Fast 3D molecular superposition and similarity search in databases of flexible molecules.

摘要: We present a new method (fFLASH) for the virtual screening of compound databases that is based on explicit three-dimensional molecular superpositions. fFLASH takes torsional flexibility database molecules fully into account, and can deal with an arbitrary number conformation-dependent features. The utilizes fragmentation-reassembly approach which allows efficient sampling conformational space. A fast clique-based pattern matching algorithm generates alignments pairs adjacent fragments rigid query molecule are subsequently reassembled to complete molecules. Using conventional features (hydrogen bond donors acceptors, charges, hydrophobic groups) we show able rapidly produce accurate medium-sized drug-like Experiments test containing diverse set 1780 (including all conformers) have shown average processing times order 0.1 seconds per be achieved PC.