DockRMSD is a program for the calculation of RMSD (root-mean-square deviation) between two poses of the same ligand molecule docked on the same protein structure without the assumption of known atomic ordering between the two files. This is achieved by recursively determining all possible atomic mappings between the two poses given their respective atomic bonding networks, and returning the mapping whose RMSD is the lowest. This is particularly relevant for comparing ligands with symmetric structure (e.g., benzene ring) as a simiple comparison based on default atomic ordering does not result in the minimum RMSD. DockRMSD does not perform any structural superposition; to calculate RMSD between two superimposed ligand conformations, see LS-align.
Note: This algorithm assumes that the two structure files represent two poses of the same ligand molecule, and that the two poses are oriented relative to aligned receptors.
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