![]() ![]() They proved that the quaternion method is equivalent to the well-known Kabsch algorithm. presented a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. The Lindemann index is a method of placing the RMSF in the context of the parameters of the system.Ī widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the RMSD. The size of this fluctuation can be measured, for example using Mössbauer spectroscopy or nuclear magnetic resonance, and can provide important physical information. When a dynamical system fluctuates about some well-defined average position, the RMSD from the average over time can be referred to as the RMSF or root mean square fluctuation. In the study of globular protein conformations, one customarily measures the similarity in three-dimensional structure by the RMSD of the Cα atomic coordinates after optimal rigid body superposition. Note that RMSD calculation can be applied to other, non-protein molecules, such as small organic molecules. In bioinformatics, the root-mean-square deviation of atomic positions, or simply root-mean-square deviation (RMSD), is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed proteins. Measure of distance between atoms of superimposed proteins ![]()
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