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Note that, for the case of ligands (contrary to proteins, as described above), their structures are most commonly not superimposed prior to the calculation of the RMSD. RMSD is also one of several metrics that have been proposed for quantifying evolutionary similarity between proteins, as well as the quality of sequence alignments.
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 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 ...
This is especially useful for rough calculations of the diffusivity in environmental systems. In some atmospheric dispersion models, the relationship between MSD and time t is not linear. Instead, a series of power laws empirically representing the variation of the square root of MSD versus downwind distance are commonly used in studying the ...
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 Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling. [1]The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations.
Methodology. By Adam Hooper and Allison Fenichel. To build this story, we tackled two problems. First, we organized millions of users’ profiles into a special format built for searching.
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.