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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. SuperPose — a protein superposition server. Uses RMSD. superpose — structural alignment based ...
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 ...
The Robotics Toolbox for Python is a reimplementation of the Robotics Toolbox for MATLAB for Python 3. [ 7 ] [ 8 ] Its functionality is a superset of the Robotics Toolbox for MATLAB, the programming model is similar, and it supports additional methods to define a serial link manipulator including URDF and elementary transform sequences.
It is certainly wide enough in my field (Bioinformatics) to be useful and pertinent. The is a lot more to the story of "RMSD" than we have in this article. It could also use a lot more math theory. I also have a programme I wrote in C for calculating RMSD (it is impressively fast) and will upload the code to this site soon.--
The sequential structure alignment program (SSAP) in chemistry, physics, and biology is a method that uses double dynamic programming to produce a structural alignment based on atom-to-atom vectors in structure space.
MassMatrix is a database search algorithm for tandem mass spectrometric data. It uses a mass accuracy-sensitive, probabilistic scoring model to rank peptide and protein matches. MassWiz Open source: MassWiz is a search algorithm developed at the Institute of Genomics and Integrative Biology that can be used as a Windows command-line tool.
The Python Package Index, abbreviated as PyPI (/ ˌ p aɪ p i ˈ aɪ /) and also known as the Cheese Shop (a reference to the Monty Python's Flying Circus sketch "Cheese Shop"), [2]: 8 [3]: 742 is the official third-party software repository for Python. [4] It is analogous to the CPAN repository for Perl [5]: 36 and to the CRAN repository for R.