Search results
Results from the WOW.Com Content Network
Quaternion – used to optimise RMSD calculations; Kabsch algorithm – an algorithm used to minimize the RMSD by first finding the best rotation [3] GDT – a different structure comparison measure; TM-score – a different structure comparison measure; Longest continuous segment (LCS) — A different structure comparison measure
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.
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 ...
Examples of correlation between RCI and other methods of measuring motional amplitudes in proteins. NMR RMSD - root mean square fluctuations of atomic coordinates in NMR ensembles, MD RMSD - root mean square fluctuations of atomic coordinates in MD ensembles, S2 - model-free order parameter, RCI - random coil index, B-factor - temperature factor of X-ray structures; RCI->NMR RMSD - root mean ...
The test functions used to evaluate the algorithms for MOP were taken from Deb, [4] Binh et al. [5] and Binh. [6] The software developed by Deb can be downloaded, [7] which implements the NSGA-II procedure with GAs, or the program posted on Internet, [8] which implements the NSGA-II procedure with ES.
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 ...
Given a transformation between input and output values, described by a mathematical function, optimization deals with generating and selecting the best solution from some set of available alternatives, by systematically choosing input values from within an allowed set, computing the output of the function and recording the best output values found during the process.
John Burkardt: Nelder–Mead code in Matlab - note that a variation of the Nelder–Mead method is also implemented by the Matlab function fminsearch. Nelder-Mead optimization in Python in the SciPy library. nelder-mead - A Python implementation of the Nelder–Mead method; NelderMead() - A Go/Golang implementation