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The study of RMSD for small organic molecules (commonly called ligands when they're binding to macromolecules, such as proteins, is studied) is common in the context of docking, [1] as well as in other methods to study the configuration of ligands when bound to macromolecules. Note that, for the case of ligands (contrary to proteins, as ...
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 test functions used to evaluate the algorithms for MOP were taken from Deb, [4] Binh et al. [5] and Binh. [6] The software developed by Deb can be downloaded, [7] which implements the NSGA-II procedure with GAs, or the program posted on Internet, [8] which implements the NSGA-II procedure with ES.
GEKKO on PyPI for Python pip install; GEKKO is open-source product of National Science Foundation (NSF) research grant 1547110; References to APMonitor and GEKKO in the literature; 18 examples of GEKKO: machine learning, optimal control, data regression; Gekko Download Statistics
Given a transformation between input and output values, described by a mathematical function, optimization deals with generating and selecting the best solution from some set of available alternatives, by systematically choosing input values from within an allowed set, computing the output of the function and recording the best output values found during the process.
Dlib is a modern C++ library with easy to use linear algebra and optimization tools which benefit from optimized BLAS and LAPACK libraries. Eigen is a vector mathematics library with performance comparable with Intel's Math Kernel Library; Hermes Project: C++/Python library for rapid prototyping of space- and space-time adaptive hp-FEM solvers.
C++ template library; binds to optimized BLAS such as the Intel MKL; Includes matrix decompositions, non-linear solvers, and machine learning tooling Eigen: Benoît Jacob C++ 2008 3.4.0 / 08.2021 Free MPL2: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Fastor [5]