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Coutsias, et al. presented a simple derivation, based on quaternions, for the optimal solid body transformation (rotation-translation) that minimizes the RMSD between two sets of vectors. [2] They proved that the quaternion method is equivalent to the well-known Kabsch algorithm . [ 3 ]
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 some disciplines, the RMSD is used to compare differences between two things that may vary, neither of which is accepted as the "standard". For example, when measuring the average difference between two time series x 1 , t {\displaystyle x_{1,t}} and x 2 , t {\displaystyle x_{2,t}} , the formula becomes
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 ...
Generally scores below 0.20 corresponds to randomly chosen unrelated proteins whereas structures with a score higher than 0.5 assume roughly the same fold. [2] A quantitative study [ 3 ] shows that proteins of TM-score = 0.5 have a posterior probability of 37% in the same CATH topology family and of 13% in the same SCOP fold family.
In computational mathematics, the Hadamard ordered fast Walsh–Hadamard transform (FWHT h) is an efficient algorithm to compute the Walsh–Hadamard transform (WHT). A naive implementation of the WHT of order n = 2 m {\displaystyle n=2^{m}} would have a computational complexity of O( n 2 {\displaystyle n^{2}} ) .
The artificial landscapes presented herein for single-objective optimization problems are taken from Bäck, [1] Haupt et al. [2] and from Rody Oldenhuis software. [3] Given the number of problems (55 in total), just a few are presented here. The test functions used to evaluate the algorithms for MOP were taken from Deb, [4] Binh et al. [5] and ...
The fast multipole method (FMM) is a numerical technique that was developed to speed up the calculation of long-ranged forces in the n-body problem.It does this by expanding the system Green's function using a multipole expansion, which allows one to group sources that lie close together and treat them as if they are a single source.