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Fitting small molecules to electron density is a challenging problem. Small molecules with few rotatable bonds are amenable to hand placement in density. Add a few rotatable bonds, however, and the problem becomes factorially more complicated. Furthermore, unlike protein modeling, many small molecules are relatively unique entities whose conformation cannot be predicted from previous homologies.
Flynn uses a high-quality conformational analysis and a fast rigid overlay to position ligands in density in conjunction with a combined forcefield to further position these conformations while, at the same time, minimizing ligand strain. Flynn can automatically locate ligand density or, failing that, use a supplied bounding box in which to place the ligands of interest.
Flynn reads common map formats such as CCP4, CNX/CNS (XPLOR) and MTZ as well as OpenEye's grid formats as well as a plethora of small molecule, protein and connection table formats.
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