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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.
In mathematics, the root mean square (abbrev. RMS, RMS or rms) of a set of numbers is the square root of the set's mean square. [1] Given a set , its RMS is denoted as either or . The RMS is also known as the quadratic mean (denoted ), [2][3] a special case of the generalized mean. The RMS of a continuous function is denoted and can be defined ...
The MSE either assesses the quality of a predictor (i.e., a function mapping arbitrary inputs to a sample of values of some random variable), or of an estimator (i.e., a mathematical function mapping a sample of data to an estimate of a parameter of the population from which the data is sampled).
In mathematics and its applications, the mean square is normally defined as the arithmetic mean of the squares of a set of numbers or of a random variable. [ 1 ] It may also be defined as the arithmetic mean of the squares of the deviations between a set of numbers and a reference value (e.g., may be a mean or an assumed mean of the data), [ 2 ...
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 molecules. [1] In the study of globular protein conformations, one customarily measures the similarity in three-dimensional ...
It is remarkable that the sum of squares of the residuals and the sample mean can be shown to be independent of each other, using, e.g. Basu's theorem.That fact, and the normal and chi-squared distributions given above form the basis of calculations involving the t-statistic:
Mean squared displacement. In statistical mechanics, the mean squared displacement (MSD, also mean square displacement, average squared displacement, or mean square fluctuation) is a measure of the deviation of the position of a particle with respect to a reference position over time. It is the most common measure of the spatial extent of ...
Standard method like Gauss elimination can be used to solve the matrix equation for .A more numerically stable method is provided by QR decomposition method. Since the matrix is a symmetric positive definite matrix, can be solved twice as fast with the Cholesky decomposition, while for large sparse systems conjugate gradient method is more effective.