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Molecular Distance Measures—a tutorial on how to calculate RMSD; RMSD—another tutorial on how to calculate RMSD with example code; Secondary Structure Matching (SSM) — a tool for protein structure comparison. Uses RMSD. GDT, LCS and LGA — different structure comparison measures. Description and services.
In fluid dynamics, normalized root mean square deviation (NRMSD), coefficient of variation (CV), and percent RMS are used to quantify the uniformity of flow behavior such as velocity profile, temperature distribution, or gas species concentration. The value is compared to industry standards to optimize the design of flow and thermal equipment ...
Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. [3] VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. [4]
A free PyMol plugin easily implementing Kabsch is . (This previously linked to CEalign , but this uses the Combinatorial Extension (CE) algorithm.) VMD uses the Kabsch algorithm for its alignment. The FoldX modeling toolsuite incorporates the Kabsch algorithm to measure RMSD between Wild Type and Mutated protein structures.
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 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.
where the median is ν, the mean is μ and ω is the root mean square deviation from the mode. It can be shown for a unimodal distribution that the median ν and the mean μ lie within (3/5) 1/2 ≈ 0.7746 standard deviations of each other. [11] In symbols, | |