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The study of RMSD for small organic molecules (commonly called ligands when they're binding to macromolecules, such as proteins, is studied) is common in the context of docking, [1] as well as in other methods to study the configuration of ligands when bound to macromolecules. Note that, for the case of ligands (contrary to proteins, as ...
In experimental psychology, the RMSD is used to assess how well mathematical or computational models of behavior explain the empirically observed behavior. In GIS, the RMSD is one measure used to assess the accuracy of spatial analysis and remote sensing. In hydrogeology, RMSD and NRMSD are used to evaluate the calibration of a groundwater ...
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 input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.
The Kabsch algorithm, also known as the Kabsch-Umeyama algorithm, [1] named after Wolfgang Kabsch and Shinji Umeyama, is a method for calculating the optimal rotation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.
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 ( 0 , 1 ] {\displaystyle (0,1]} , where 1 indicates a perfect match between two structures (thus the higher the better ...
The RMS value of a set of values (or a continuous-time waveform) is the square root of the arithmetic mean of the squares of the values, or the square of the function that defines the continuous waveform.
This definition for a known, computed quantity differs from the above definition for the computed MSE of a predictor, in that a different denominator is used. The denominator is the sample size reduced by the number of model parameters estimated from the same data, ( n − p ) for p regressors or ( n − p −1) if an intercept is used (see ...
With the availability of high numbers of genomic sequences it becomes feasible to analyze such sequences for coevolving residues.The effectiveness of this approach results from the fact that a mutation in position i of a protein is more likely to be associated with a mutation in position j than with a back-mutation in i if both positions are functionally coupled (e.g. by taking part in an ...