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Typically RMSD is used as a quantitative measure of similarity between two or more protein structures. For example, the CASP protein structure prediction competition uses RMSD as one of its assessments of how well a submitted structure matches the known, target structure. Thus the lower RMSD, the better the model is in comparison to the target ...
In bioinformatics, the root mean square deviation of atomic positions is the measure of the average distance between the atoms of superimposed proteins. In structure based drug design, the RMSD is a measure of the difference between a crystal conformation of the ligand conformation and a docking prediction.
Let P and Q be two sets, each containing N points in .We want to find the transformation from Q to P.For simplicity, we will consider the three-dimensional case (=).The sets P and Q can each be represented by N × 3 matrices with the first row containing the coordinates of the first point, the second row containing the coordinates of the second point, and so on, as shown in this matrix:
The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the ...
The RMS over all time of a periodic function is equal to the RMS of one period of the function. The RMS value of a continuous function or signal can be approximated by taking the RMS of a sample consisting of equally spaced observations. Additionally, the RMS value of various waveforms can also be determined without calculus, as shown by ...
The TM-score is intended as a more accurate measure of the global similarity of full-length protein structures than the often used RMSD measure. The TM-score indicates the similarity between two structures by a score between (,], where 1 indicates a perfect match between two structures (thus the higher the better). [1]
Essentially the CV(RMSD) replaces the standard deviation term with the Root Mean Square Deviation (RMSD). While many natural processes indeed show a correlation between the average value and the amount of variation around it, accurate sensor devices need to be designed in such a way that the coefficient of variation is close to zero, i.e ...
Homology model of the DHRS7B protein created with Swiss-model and rendered with PyMOL. Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").