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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 ]
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:
RMSD is a measure of accuracy, to compare forecasting errors of different models for a particular dataset and not between datasets, as it is scale-dependent. [1] RMSD is always non-negative, and a value of 0 (almost never achieved in practice) would indicate a perfect fit to the data. In general, a lower RMSD is better than a higher one.
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.
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.
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 ...
Source code for algorithm implementations, and TLE interpretation in some cases: python-sgp4 A Python Implementation of the sgp4 model with automatic downloading of TLE Elements from NORAD database. PHP5 based on Gpredict; Java: SDP4 and predict4java; C++, FORTRAN, Pascal, and MATLAB. go-satellite GoLang implementation of SGP4 model and helper ...
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 ...